A boy of nine arrives in southern Punjab carrying a small cloth bundle. His father, a tenant farmer near Rahim Yar Khan, can no longer feed him. The seminary at the edge of the village offers free room, free food, and free education in the Quran. The boy enters at age nine. He emerges fifteen years later as a foot soldier in Lashkar-e-Taiba. The path between those two moments is what Pakistani counter-terror officials, Indian intelligence assessments, and Western academic studies have come to call the madrassa-to-militant pipeline. It is not a metaphor. It is a deliberately constructed conveyor that takes in poverty and outputs ideologically committed fighters, and it is the single mechanism that allows Pakistan’s terror organizations to regenerate their ranks faster than the shadow war can eliminate them.

Most coverage of Pakistan’s seminary system gets the framing wrong in two opposite directions. Western media tends to describe the entire ecosystem as a “terror factory,” ignoring the millions of Pakistani families for whom these institutions provide the only available education. Pakistani official discourse tends to insist that all seminaries are benign religious institutions, ignoring the documented cases where specific networks have produced specific fighters who have carried out specific attacks. Both framings fail because both miss the architecture. The pipeline is not the entire madrassa system. The pipeline is a specific subset of seminaries operated by Jamaat-ud-Dawa, Jaish-e-Mohammed, and a handful of allied networks, embedded within the larger system in a way that gives them legal and social cover while serving a function the broader system does not. This article maps that subset. It distinguishes the militant pipeline from the wider seminary ecosystem, traces the four-stage conversion process from rural enrollment to operational fighter, and assesses whether the targeted killings now reaching deep into Karachi and Sindh can outpace the replacement rate the seminaries are designed to sustain.

The argument is straightforward. Pakistan’s madrassa network is not an incubator of extremism by accident. A specific subset within the network is a deliberately constructed pipeline, where the curriculum is designed to produce fighters rather than scholars, where the financial flows are routed to ensure the seminaries answer to the parent terror organization rather than to the state, and where the geographic clustering tracks not population centres but historical recruitment grounds. The shadow war kills operatives one by one. The pipeline replaces them by the hundred. Until the pipeline itself is shut, every elimination is a single subtraction from a number that the seminaries continually replenish.

Origins and Founding

The madrassa system in the territory that became Pakistan dates to the eighteenth century, with Deoband itself established in 1866 in what is now Uttar Pradesh, India. For more than a century after that, the seminaries served the function their founders intended. They produced ulema, the religious scholars who interpreted Islamic law for their communities, who issued fatwas on questions of inheritance and ritual, who staffed the mosques and the qazi courts, and whose graduates went on to teach in the next generation of seminaries. The curriculum, organised around the Dars-i-Nizami syllabus that crystallised in the late seventeenth century, emphasised tafseer, hadith, fiqh, and Arabic grammar. There was nothing in this system as originally constituted that produced fighters.

The transformation began in 1979 and was largely complete by 1989. The proximate cause was the Soviet invasion of Afghanistan in December 1979 and the decision by General Mohammad Zia-ul-Haq, who had seized power in a 1977 coup, to position Pakistan as the front-line state in the resulting jihad. The strategic logic was geopolitical. Zia needed a population mobilised to resist Soviet expansion southward. The funding logic was financial. The CIA’s Operation Cyclone channelled billions of dollars through Pakistan’s Inter-Services Intelligence Directorate to support the Afghan resistance, and Saudi Arabia matched American funding roughly dollar for dollar. The implementation logic was institutional. Zia chose the seminaries as the mobilisation infrastructure because they were already in place, already had social legitimacy, and already enjoyed exemption from the secular school inspections that would have made other institutions more administratively legible.

What followed was the deliberate extremisation of a system that had been, for the most part, doctrinally conservative but politically inert. The number of registered seminaries in Pakistan grew from roughly 900 at the time of partition to several thousand by the end of Zia’s rule in 1988, and continued growing afterward. The estimates vary because the reporting methodologies vary, but the overall trajectory is undisputed. Pakistan’s first official economic survey to count seminaries put the figure at 36,331 by the time of the 2023 census. Earlier estimates suggested 12,000 to 40,000 across various points in the 2000s and 2010s, with much of the divergence reflecting the gap between registered seminaries and the larger universe of unregistered institutions. The 9/11 Commission report later identified the schools as recruiting grounds for jihadist organisations, citing this trajectory as one of the structural conditions enabling the emergence of al-Qaeda within Pakistan’s tribal periphery.

The Zia regime did not simply allow the seminaries to grow. It actively reshaped what they taught. Curricula were adjusted to emphasise the duty of jihad as a personal obligation rather than a collective one. Standard Deobandi texts that had treated jihad as a defensive obligation responding to specific aggression were supplanted in radical seminaries by a reading that emphasised expansionist obligation. Boys were taught that apostasy and polytheism were punishable by death, that only Muslims had the right to rule, and that the modern sovereign nation state was itself a form of polytheism incompatible with Islam. The ideological framework that emerged from this reshaping made every Soviet conscript in Afghanistan a legitimate target, every secular Pakistani official a potential apostate, and every Indian Muslim who acquiesced in non-Muslim rule a religious failure to be either reformed or punished. The framework did not require the boys to read theology critically. The framework required only that they accept it. The system was structured so that those who accepted it were rewarded with status and those who questioned it were not.

By the time the Soviet army withdrew from Afghanistan in February 1989, the seminary infrastructure had produced something neither Zia nor his American backers had fully anticipated. They had produced an ideologically organised, militarily trained, and self-reproducing population of fighters who saw themselves as continuing a religious obligation that had no defined endpoint. The Soviets were gone. The fighters and the seminaries remained. The Pakistani state, having unleashed this force in the name of geopolitics, now had to find new battlefields for it. The closest available was Indian-administered Kashmir, where an indigenous insurgency had erupted in 1989. The Pakistani military’s Inter-Services Intelligence channelled the seminary-trained fighters across the Line of Control. The result was the rapid replacement of the original Kashmiri insurgent groups, which were largely secular and ethno-nationalist, by Pakistani-controlled jihadist organisations whose recruits came overwhelmingly from the seminaries.

The two organisations that would become the principal antagonists of the shadow war emerged directly from this transition. Lashkar-e-Taiba was founded in 1986 in Kunar, Afghanistan, by Hafiz Saeed and Zafar Iqbal, with Abdullah Azzam playing an early ideological role. Its institutional centre, the Markaz Dawat-ul-Irshad, registered as a seminary and charitable organisation, gave the group its civilian face and its recruitment infrastructure from the outset. Jaish-e-Mohammed was founded in January 2000 by Masood Azhar, weeks after his release in the IC-814 hostage crisis, and immediately set about building seminaries in Bahawalpur as the operational and recruitment base. Both organisations were structured from inception to function as state-aligned jihadist projects with seminary fronts, not as militias that later acquired charitable wings. The seminaries were not added later. The seminaries were the foundation.

This founding history matters because it determines what reform can and cannot achieve. A militant network that grew out of an originally apolitical seminary tradition might in principle be peeled back, restoring the seminaries to their original function. A militant network that was structured from inception around seminary recruitment cannot be peeled back without dismantling the institutions themselves, because the institutions were never anything else. The seminaries that feed the broader definitive guide to Lashkar-e-Taiba’s structure and operations are not LeT-adjacent. They are LeT. The seminaries that feed the JeM organisational guide are not JeM-adjacent. They are JeM. Reform efforts that proceed on the assumption that there is a seminary core to be saved from a militant fringe miss the architectural reality. There is no separable core. There is a parent organisation that owns the seminaries and uses them for its institutional purposes, and that purpose, since the founding of these organisations in the 1980s and 1990s, has always been the production of fighters.

Ideology and Objectives

The seminaries within the militant pipeline are not ideologically uniform with the wider Pakistani religious educational system, and this distinction is the single most important fact for any analysis that hopes to be accurate rather than polemical. Most Pakistani seminaries belong to one of five maslak, or sectarian schools: Deobandi, Barelvi, Ahl-e-Hadith, Shia, and Jamaat-e-Islami. Each maslak has its own curriculum boards, its own educational authorities, and its own sectarian identity. Roughly forty-four percent of seminaries follow the Deobandi school, around twenty-five percent the Barelvi tradition, six to seven percent the Ahl-e-Hadith school, and the remainder the Shia and Jamaat-e-Islami traditions. The militant pipeline overwhelmingly draws from two of these five schools: Deobandi and Ahl-e-Hadith. Barelvi seminaries, despite forming a quarter of the total, produce almost no fighters for the principal jihadist groups, in part because the Barelvi tradition’s veneration of saints and shrines is the very thing the Deobandi and Ahl-e-Hadith strands consider polytheistic.

The Ahl-e-Hadith school produces the LeT recruit. The doctrine emphasises strict monotheism, rejects all four classical Sunni law schools as later innovations, and insists on direct return to the Quran and hadith as the only legitimate authorities. Politically, the school has historically been quietist, but the LeT-aligned wing under Hafiz Saeed reinterpreted the tradition to make armed jihad the highest form of religious obligation. The seminary curriculum within the LeT network reflects this reinterpretation. Students are taught that the recovery of historically Muslim lands lost to non-Muslim rule is not optional but obligatory, that the most important such land is Kashmir, that defensive jihad against an occupying power is a personal duty incumbent on every adult male Muslim, and that the obligation supersedes parental consent, marriage, employment, or any other competing claim on the boy’s life. The curriculum does not present these as one view among several. It presents them as the only correct understanding of orthodox Islam.

The Deobandi seminaries that feed the JeM pipeline operate within a different doctrinal frame but arrive at functionally similar outputs. Deobandi theology, named for the seminary at Deoband founded in 1866, was historically a reform movement seeking to purify South Asian Islam from what its founders saw as Hindu and Sufi accretions. Its core concerns were doctrinal rather than political, but the political mobilisation of Deobandi institutions during the Afghan jihad of the 1980s permanently altered the school’s institutional culture. The Deobandi seminaries that became JeM-aligned, especially those connected to the Banuri Town complex in Karachi, the Jamia Uloom-ul-Islamia, integrated jihadist content into a curriculum that was already structured around the elimination of non-orthodox practice. The result was a doctrine in which jihad against external enemies, primarily India, was placed within a larger framework of jihad against internal religious deviation, primarily Shia Muslims, Sufi shrine practitioners, and Barelvi traditionalists. This is why the JeM and its allied Deobandi networks produced fighters who attacked both Indian targets and Pakistani Shia communities, in some cases the same fighters across both target sets.

The objectives that the militant pipeline trains its students to pursue are not ambiguous. The seminaries within the LeT network openly state, through Hafiz Saeed’s preserved sermons and Markaz publications, that the goal is the liberation of Kashmir, the eventual breakup of India, and the establishment of an Islamic order across the entire South Asian subcontinent. The seminaries within the JeM network, through Masood Azhar’s published writings including his book “Fazail-e-Jihad,” articulate similar objectives with somewhat more emphasis on the religious duty of all Muslims to participate in jihad as a continuing obligation rather than a one-time campaign. Both networks treat Pakistan’s accommodation with India, including the Shimla Agreement and any subsequent peace processes, as religious betrayals. Both networks treat Pakistani officials who advocate accommodation as suspect at best and apostate at worst.

This ideological frame produces specific behavioural commitments that the seminaries instil during the training period. Boys are taught that the obligation of jihad supersedes the obligation to obey parents, which is why families who attempt to retrieve sons from radical seminaries often find themselves told that the son has already taken religious commitments that the family cannot countermand. Boys are taught that the obligation of jihad supersedes the obligation to marry and have children, which is why fighters are often dispatched on missions before they reach the age at which their families would arrange marriages, and why those who survive the missions return to find their original communities strangers. Boys are taught that the obligation of jihad creates a brotherhood among fighters that supersedes the natural brotherhood of family. The institutional purpose of these teachings is to detach the recruit from any social network that might compete with the organisation. The detachment is not an unintended side effect of the training. The detachment is the training.

The ideology imported from these seminaries is what makes the recruit operationally useful even when his technical skills are limited. A trained sniper who lacks the conviction to die for his cause is a weak asset. A poorly trained nineteen-year-old who is convinced that death in jihad guarantees paradise is, paradoxically, a stronger asset for many missions, because the organisation does not need to plan for his exfiltration. The 26/11 attackers, dispatched by LeT to Mumbai in November 2008, were largely seminary-trained recruits in their late teens and early twenties. None of the operational team was extracted. All ten were killed during the attacks except one, Ajmal Kasab, who was captured. The post-mortem analysis of their behaviour during the attacks revealed remarkably little operational sophistication but extraordinary ideological commitment. They prayed during the attacks. They expected to die. They had been told, and they had believed, that this was the highest religious vocation available to them. The seminary that produced these expectations, not the rifle range that taught them to handle weapons, was the asset that made the attack possible.

Organisational Structure

The seminary networks that constitute the militant pipeline are not loosely affiliated institutions that happen to share an ideology. They are organisationally integrated systems with formal command relationships, shared funding mechanisms, coordinated curricula, and planned geographic distributions. Understanding the structure requires distinguishing four levels: the parent terror organisation, the institutional centre, the regional flagship seminaries, and the village feeder seminaries.

At the level of the parent terror organisation, both LeT and JeM operate the seminary networks as wholly owned subsidiaries. LeT exercises this control through the Markaz Dawat-ul-Irshad, which was renamed Jamaat-ud-Dawa, then renamed again to Falah-i-Insaniyat Foundation under sanctions pressure, while preserving the same personnel, the same finances, and the same operational seminaries throughout the renamings. JeM exercises this control more directly, with Masood Azhar himself and his immediate family, including his brother Abdul Rauf Asghar, holding the senior administrative positions across the seminary network. Both organisations have boards or shura councils that include the senior religious figures of the network alongside the operational leadership of the militant wing. There is no firewall. The same individuals who decide which boys to send for advanced military training are also the individuals who decide which seminaries to expand and which curricula to adopt.

At the level of the institutional centre, each network has a flagship campus that serves as the doctrinal and administrative headquarters. For LeT, this is Markaz-e-Taiba in Muridke, a two-hundred-acre complex outside Lahore that combines a seminary, a mosque, a hospital, dormitories, agricultural land, and reported tactical training grounds. For JeM, the institutional centre is the Madrassa Usman-o-Ali in Bahawalpur, with the adjacent Jamia Masjid Subhanullah expanded by Abdul Rauf Asghar’s land acquisitions in 2022 to encompass a larger campus footprint. Both centres function simultaneously as religious seminaries that the parent organisation cites when defending its civilian character and as command-and-control hubs that the parent organisation uses for the actual coordination of the militant network. The dual function is not concealed. The dual function is the design.

At the level of the regional flagship seminaries, each network operates a smaller number of large institutions in major Pakistani cities that serve as recruitment funnels for their surrounding districts. JuD operated approximately three hundred such seminaries across Pakistan at the peak of its registered presence, with concentrations in Punjab and Sindh and a smaller footprint in Khyber Pakhtunkhwa. JeM’s regional seminary network is smaller in absolute number but more geographically concentrated, with the Bahawalpur core radiating into surrounding districts of southern Punjab including Rahim Yar Khan, Multan, and Dera Ghazi Khan. These regional flagships typically house several hundred to a thousand students, employ ten to thirty teachers, and maintain connections both upward to the institutional centre and downward to the village feeder seminaries that funnel students to them.

At the level of the village feeder seminaries, the network expands to several thousand small institutions, often single-room operations attached to a village mosque, that conduct the initial enrolment and the early stages of religious education. These village feeders are where the rural poor send their sons. The teacher is often a graduate of one of the regional flagships, returned to his home village to teach. The curriculum at this level is largely indistinguishable from that of any conservative Sunni seminary, focused on Quranic memorisation, basic Arabic, and elementary fiqh. What distinguishes the feeder from a politically inert seminary is not what is taught at age nine but what happens at age fifteen or sixteen. Students at the village level who show religious aptitude and ideological promise are selected for transfer to the regional flagship. Those who do not fit the profile, who show too much interest in their families, who question what they are taught, or who demonstrate insufficient commitment, are simply graduated and returned to ordinary life as low-level clerics or village imams. The pipeline is selective from the start.

The geographic distribution of the militant pipeline tracks four specific regions of Pakistan with high precision. Southern Punjab, especially the districts of Bahawalpur, Rahim Yar Khan, Muzaffargarh, Dera Ghazi Khan, and Multan, hosts the densest concentration of JeM-aligned seminaries. The region’s combination of agricultural poverty, weak state presence, large rural population, and traditional religious conservatism makes it ideal recruitment territory. Central Punjab, particularly Lahore, Sheikhupura, Sialkot, and Gujranwala, hosts the densest concentration of LeT-aligned seminaries, with Muridke as the institutional anchor. Sindh province, especially the urban centres of Karachi and Hyderabad along with smaller centres in Nawabshah and Khairpur, hosts a substantial JuD presence woven into the migrant labour networks of the province. Khyber Pakhtunkhwa, especially the southern districts and the former tribal areas, hosts a smaller but operationally significant network linked more closely to Afghan-oriented groups and the Haqqani complex than to the principal anti-India organisations.

This geographic distribution is consequential because it tells us where the eliminations would have to occur to dismantle the recruitment infrastructure rather than merely prune the operational fighters. A targeted killing campaign that eliminates LeT operatives in Karachi without addressing the Muridke campus that produced them addresses the symptom rather than the cause. The shadow war’s recent turn toward Sindh, evidenced by the killing of Sardar Hussain Arain in Nawabshah, suggests intelligence services have begun mapping the seminary infrastructure with increasing granularity. Arain was not a senior LeT operative in any operational sense. He was a regional administrator of JuD’s seminary network in Sindh. His elimination signals targeting of the recruitment apparatus rather than just the fighters it produces. Whether this signals a broader shift in doctrine remains to be seen.

The organisational structure also produces a specific pattern of resilience. Because the seminaries operate at multiple levels with redundant capacity, the elimination of any single institution does not collapse the system. The closure of a regional flagship temporarily disrupts the conversion of village students to organisational fighters, but the village feeders continue producing potential recruits, and another regional flagship can absorb the surplus. The killing of any single administrator removes one functioning node but does not interrupt the broader flow. This is why the pipeline has survived multiple Pakistani crackdowns, including the post-2014 National Action Plan and the post-2019 Pulwama crackdown, and why it continues operating despite the sustained pressure of the shadow war. The system is not centralised at any single point that could be permanently destroyed. It is distributed across thousands of institutions whose individual closure means almost nothing.

Funding and Recruitment

The financial architecture that sustains the militant pipeline operates through three distinct streams, each of which has been documented by Pakistani regulatory filings, FATF mutual evaluation reports, and Indian intelligence assessments. Understanding these streams is essential because each requires different countermeasures and each presents different vulnerabilities.

The first stream is domestic charitable collection inside Pakistan, which the seminaries collect through animal-hide donations during Eid-ul-Adha, through donation boxes placed at shops and bus terminals, through door-to-door collection drives during Ramadan, and through the zakat that pious Pakistani Muslims pay annually as religious obligation. The animal-hide trade is particularly significant. During the three days of Eid-ul-Adha each year, Pakistani Muslims slaughter sheep, goats, cows, and camels in fulfilment of religious obligation. The hides from these slaughtered animals are donated to charitable organisations that sell them to the leather industry. JuD historically collected hides at scale, with operations reportedly extending to several hundred thousand hides per year at peak, generating revenue that flowed into the seminary network’s operating budget. The hide collection was always semi-formal, conducted through volunteer networks rather than regulated charities, which made it both lucrative and difficult to track.

The donation-box and bus-collection mechanisms operate similarly. Sindh authorities, in their geo-tagging exercise that identified more than ten thousand so-called ghost madrassas across the province, found that many of these phantom institutions existed primarily as fundraising fronts. They had registered names, registered bank accounts, and active donation boxes in markets and bus terminals across major Sindh cities, but they had no actual students, no actual buildings, and no actual instruction. The donations they collected flowed not to seminary operations but directly to the parent terror organisation’s operational accounts. This pattern, replicated across Punjab and Sindh, generated tens of millions of dollars annually that the seminaries used both to operate the institutions where students actually studied and to supplement the financial flows of the parent organisations.

The second stream is foreign donations, which historically came through three principal channels: Saudi and Gulf state donors with sympathy for Sunni revivalist causes, Pakistani diaspora communities in the Gulf, the United Kingdom, and North America, and during the 1980s and 1990s the United States itself through the Afghan jihad funding that bled into seminary support. The Saudi channel was particularly important during the 1980s and 1990s, with funding flowing both through formal Saudi governmental and royal-family charity foundations and through informal networks of private Saudi donors. The 9/11 Commission report documented the role of Saudi-origin funding in supporting the Pakistani seminary network during this period. Saudi government policy has shifted significantly since 2017, with Crown Prince Mohammed bin Salman publicly distancing the kingdom from religious export programmes, but the historical infrastructure that the Saudi flows built remains in place, and private donors with personal sympathies have continued some level of contribution.

The diaspora channel operates through informal value transfer systems, particularly hawala, that allow Pakistani expatriate workers to send funds home outside the formal banking system. A Pakistani worker in Dubai who wishes to donate to a Lahore seminary can deposit cash with a hawala dealer in Dubai, who notifies a counterpart in Lahore to disburse the equivalent amount minus a small fee. The transaction never crosses the formal financial system, leaves no banking trail, and is impossible to monitor through standard counter-terrorism finance tools. The 9/11 Commission report described this mechanism in detail. JuD officials documented as having travelled to Saudi Arabia seeking donations for new schools were found to have inflated school construction costs to donors and siphoned excess funds to militant operations, a pattern that the seminary front made possible because the actual existence of the schools was verifiable while the actual costs were not.

The third stream is state subsidy, which Pakistani governments have provided to the broader seminary system in various forms over decades. Some of this subsidy is provided directly through the Auqaf departments of provincial governments, which administer religious endowments. Some is provided through tax exemptions on charitable activities. Some is provided indirectly through provision of land, water, electricity, and other utilities at concessional rates. The seminaries that constitute the militant pipeline have benefited from these state subsidies alongside the broader system, even when the parent organisation has been formally banned. The Pakistani state’s reluctance to interrupt these subsidies, even at moments when international pressure intensifies, reflects the political calculation that a sustained confrontation with the seminary lobby would impose unacceptable domestic costs.

The recruitment side of the pipeline operates through mechanisms that are sociologically more interesting than the funding side. The seminaries do not recruit students primarily through ideological appeal. They recruit through economic offer. A family in southern Punjab whose son has reached age seven or eight faces a choice. The local government school, where one exists, often lacks teachers, lacks textbooks, charges nominal fees the family cannot afford, and offers a curriculum that the family cannot help with. The local seminary, by contrast, is free, provides food and lodging, requires no transportation cost, and offers a curriculum the family understands. The choice for an impoverished family is not between secular education and religious education. The choice is between religious education and no education. The seminary, even when its long-term outputs are problematic, is the option the family can actually afford.

This economic logic explains why the recruitment pipeline cannot be shut by policing alone. Even if every militant-aligned seminary in Pakistan were closed tomorrow, the underlying conditions that drive families to enrol their sons would remain unchanged. Pakistan’s public education system, despite improvements over the past two decades, still does not reach the rural poor in a substantive way. Adult literacy in southern Punjab and rural Sindh remains below sixty percent. The teacher-to-student ratio in functioning rural government schools is often above one-to-fifty. The dropout rate after primary school exceeds forty percent in many districts. The seminaries fill an educational vacuum that the state has not filled. Closing the seminaries without filling the vacuum produces not educated children but uneducated children, who become a different category of social problem rather than the same problem solved.

The recruitment pipeline also exploits specific features of Pakistani family structure. Families with multiple sons typically distinguish between the eldest son, who will inherit land and family responsibilities, and younger sons, who must find their own way. The younger son is more likely to be sent to a seminary precisely because the family has less to lose if the son becomes a religious scholar with limited employment prospects. The seminary recruiters understand this calculus perfectly and structure their outreach to target younger sons. The radicalisation literature has documented this pattern across multiple militant organisations: the operational fighters are disproportionately younger sons of large families, with the seminary network providing them an alternative life trajectory that their economic position would otherwise have foreclosed.

The conversion from religious student to organisational fighter does not happen at a single moment. It happens across years, through a graduated sequence that the seminaries have refined over four decades. The boy who arrives at age nine begins with Quranic memorisation, conducted in Arabic he does not yet understand. By age twelve, he has memorised substantial portions of the Quran and has begun studying Arabic grammar and basic Islamic jurisprudence. By age fifteen, he has been exposed to the political content that distinguishes the militant pipeline from the broader system: the hadith collections selected to emphasise jihad, the contemporary writings of the network’s senior figures, the reframing of Pakistani history as a continuous struggle against non-Muslim aggression. By age seventeen, those students who have been selected for further development are introduced to the operational network. The introduction is not abrupt. It comes through teacher recommendations, through summer camps that combine religious study with physical fitness, through invited talks by visiting jihadi figures who frame their own biographies as templates the students might follow. By age twenty, the selected student is a candidate for the parent organisation’s military training programmes. By age twenty-two or twenty-three, he is operationally deployable, either as a fighter for cross-border infiltration into Kashmir or, less commonly, as a recruit for international operations.

Each stage of this conversion has its own institutional logic and its own selection mechanism. Students who fail to advance from one stage to the next are not punished or expelled. They are simply graduated as ordinary religious students, with a competence in religious instruction that allows them to return to their home villages as imams and teachers. This branching, where the rejected candidates become the next generation of village teachers, creates a feedback loop in which the failed pipeline candidates expand the network’s social footprint even when they do not become fighters themselves. A village imam who graduated from a JuD-aligned seminary, who himself never went to military training, will nonetheless be more likely to identify and recommend the next generation of his village’s brightest religious students for the same pipeline that processed him. The pipeline reproduces itself through both its successes and its rejections.

Major Operations

The conversion process from rural student to operational fighter, when reconstructed across multiple documented cases, falls into four distinguishable stages: enrolment, conditioning, preparation, and handoff. Each stage has its own typical duration, its own primary location, its own institutional handlers, and its own indicators of progression. Each stage also has its own failure modes, where boys who would otherwise have advanced fall out of the pipeline either by their own choice, by family intervention, or by selection decisions made by the seminary administrators.

Stage 1: Enrolment

The first stage typically extends from age seven or eight through age twelve or thirteen. During this period, the recruit is a village seminary student in his home district, sleeping in the seminary’s dormitory or returning each evening to his family. The curriculum is heavily focused on Quranic memorisation, with the explicit objective that the student should commit substantial portions of the Quran to memory. The pedagogical method is repetitive recitation, with teachers correcting pronunciation and rhythm rather than explaining meaning. Most students at this stage do not understand much of what they are reciting because the Arabic of the Quran is grammatically complex and the boys are not yet receiving systematic Arabic grammar instruction. The recitation nonetheless produces a deep familiarity with the cadences and rhythms of the text, which becomes the foundation for the later ideological instruction.

What is significant about this stage is what is not yet happening. The boys are not being told that they will become fighters. They are not being introduced to the parent organisation’s senior figures. They are not receiving political content. The institutional posture of the seminary toward families in this period is calculated reassurance: the boy is becoming pious, the boy is learning the Quran, the boy is acquiring a religious vocation that will give him social standing. Families who visit the seminary find what they expected to find, religious instruction in a religious institution. The boys who advance to the next stage are selected during this period based on observed characteristics. Aptitude for memorisation matters. Discipline matters. Social isolation, the willingness to spend time with the seminary community rather than with family, matters. Religious fervour, evidenced by extended prayer and visible attentiveness to teachers, matters. Boys who display these characteristics are flagged by the village teacher for advancement.

Stage 2: Conditioning

The second stage typically extends from age twelve or thirteen through age fifteen or sixteen. The recruit is now studying at a regional flagship seminary, often in a different district or province from his home, separated from his family by physical distance and by the routine of seminary life. The curriculum has shifted. Quranic memorisation continues but is now joined by systematic Arabic grammar instruction, hadith study, and elementary jurisprudence. More significantly, the political content begins. Students are introduced to the contemporary writings of the network’s senior figures. They study selected hadith collections that emphasise jihad as religious obligation. They are taught a version of South Asian history that frames the experience of Muslims under non-Muslim rule as a continuous emergency requiring religious response. They watch carefully selected video content during designated periods, including footage of jihad theatres in Kashmir and elsewhere. They hear sermons by visiting figures whose biographies model the trajectory the students themselves might follow.

The conditioning at this stage is not crude. The seminary does not simply tell the students that they will fight in Kashmir. The seminary creates an intellectual frame in which the question “what does my faith require of me” naturally produces the answer “to participate in the defence of Muslim lands.” The frame is built up over years through repeated exposure rather than imposed in a single conversion moment. By the time the boy is sixteen, the question has become natural and the answer has become his own. He believes that he has reached this conclusion through his own religious reflection. The seminary has structured the inputs so that this conclusion was the only one his reflection could plausibly reach, but he experiences it as personal religious certainty rather than as institutional indoctrination. The distinction matters because operatives who experience their commitment as personal are more reliable than operatives who experience it as imposed.

The detachment from family also intensifies during this stage. Visits home become less frequent. The boy’s social networks shift toward seminary classmates. His ordinary patterns of speech, dress, and reference change. When he visits home, his family notices that he has become a stranger, more religious than they are, less interested in family gossip, more focused on questions of religious correctness. Some families respond to these changes by attempting to retrieve the boy. The seminary’s response in such cases is calibrated. Direct refusal would expose the institution. Instead, seminary administrators typically argue that the boy himself wishes to continue his studies, that he is making religious progress that should not be interrupted, that the family’s intervention would damage the boy’s religious vocation. In some cases, the boy himself, by this stage, will have internalised the seminary’s framing sufficiently that he resists family efforts to remove him. The seminary has not kidnapped the boy. The seminary has made the boy into a person who does not wish to leave.

Stage 3: Preparation

The third stage typically extends from age fifteen or sixteen through age eighteen or nineteen. The recruit has now been selected for further development beyond ordinary seminary graduation. He has been moved either to a more advanced seminary or to one of the institutional centres of the network, either Markaz-e-Taiba in Muridke for LeT recruits or one of the JeM Bahawalpur facilities for JeM recruits. The curriculum has shifted again. Theological study continues but now includes specific texts written by the network’s senior figures, including Hafiz Saeed’s collected sermons for LeT recruits and Masood Azhar’s published works including “Fazail-e-Jihad” for JeM recruits. The recruits also begin systematic physical preparation. Daily exercise becomes part of the institutional routine. Long hikes, often through difficult terrain, are framed as both physical conditioning and religious discipline. Wrestling and unarmed combat are introduced as practical skills that pious men should possess.

Crucially, this stage also includes the recruit’s first sustained exposure to figures who themselves have operational experience. Returning fighters, debriefed and theologically validated, address the recruits about their experiences. Senior figures with operational portfolios visit the institution and speak about the strategic logic of the campaign. The recruits begin to see themselves as candidates for the next phase of the network’s work rather than as religious students whose vocation is internal to the seminary. The institutional rhetoric reinforces this self-conception. The recruits are addressed as future mujahideen rather than as students. They are given honorific forms of address normally reserved for those who have completed combat tours. The status hierarchy of the institution is restructured to make participation in the operational network the highest status and ordinary religious scholarship a lower status.

By the end of this stage, the recruits have made what counter-terrorism analysts describe as the cognitive transition. They no longer think of themselves as boys from villages who happened to attend a seminary. They think of themselves as members of the parent organisation’s broader project, with a future that connects to the campaign in Kashmir, the recovery of Muslim lands, and the religious obligation that frames the network’s institutional purpose. This cognitive transition is more important than any specific tactical skill the recruits will later acquire. A recruit who has made this transition can be trained to operate weapons, to plan attacks, to function in cells. A recruit who has not made this transition cannot be reliably deployed, no matter how well he can shoot.

Stage 4: Handoff

The fourth stage is the briefest but the most operationally consequential. The recruit, now eighteen to twenty years old, is transferred from the seminary network to the parent organisation’s military training infrastructure. For LeT recruits, this typically means transfer to one of the training camps in Pakistan-administered Kashmir, including the facilities reportedly operated near Muzaffarabad, in the Neelum Valley, and at locations along the Line of Control. For JeM recruits, the training infrastructure historically included camps at Balakot, struck by Indian aircraft in February 2019 in the Balakot strike retaliation following the Pulwama attack, as well as other facilities in PoK and the tribal areas. The training at these camps is functionally military: weapons handling, small unit tactics, infiltration techniques across mountainous terrain, operation in cells that maintain communication discipline, and the specific skills required for the attack types the parent organisation typically conducts.

The transition from seminary to training camp is typically accompanied by formal initiation. The recruit takes a bayat, an oath of allegiance, to the parent organisation’s commander. The bayat is religious in form and binding in ideological terms: the recruit pledges his life to the cause and accepts that the parent organisation now has authority over his religious obligation. The transition is also accompanied by separation from the seminary identity. The recruit may take a nom de guerre. He may be deployed under multiple identities depending on the operational context. He receives the network’s communication codes, the protocols for contact with handlers, the procedures for disengagement and reconnection if a mission is compromised. The seminary student who entered the campus seven or eight years earlier has become a new person, with a new name, a new institutional affiliation, and a new vocational identity, all of which are wholly owned by the parent organisation.

The handoff stage is also where the failure rate becomes most visible. Some recruits who completed the conditioning and preparation stages successfully nonetheless fail at the handoff. They may have qualms about the actual prospect of killing or being killed that did not surface during the abstract discussion of jihad. They may have family circumstances, an aging parent, an arranged marriage, that pull them back from the final commitment. They may simply lack the physical or psychological constitution that operational deployment requires. The parent organisation has procedures for handling these cases. The recruits who fall out at this stage are typically not punished but are reassigned to seminary positions, where they continue serving the broader network as teachers, fundraisers, or recruitment specialists. Their conditioning, even when it has not produced an operational fighter, has produced a network asset of a different kind.

State Sponsorship and Protection

The militant pipeline could not have grown to its current scale or operated with its current freedom without the active complicity of significant elements within the Pakistani state. This complicity has taken multiple forms across multiple decades, and unpacking it requires distinguishing between the formal state, which periodically commits to crack down on the seminaries, and the parallel state, the institutions and personnel within Pakistan’s security and religious establishments who have maintained the pipeline as a strategic asset.

The Inter-Services Intelligence Directorate has been the most documented institutional sponsor. ISI involvement with the seminary network dates to the 1980s Afghan jihad, when the agency served as the conduit through which CIA and Saudi funding flowed to the Afghan resistance and through which seminary recruits were directed to the resistance camps. The institutional habits formed during this period persisted after the Soviet withdrawal, with ISI redirecting seminary outputs from the Afghan theatre to the Kashmir theatre after 1989. By the mid-1990s, the relationship between ISI’s S-Wing, the directorate responsible for proxy warfare, and the LeT and JeM seminary networks had become structural rather than incidental. S-Wing officers maintained ongoing liaison with the seminary administrations. They assisted with logistics for moving recruits across the Line of Control. They provided cover for senior figures within the seminary network when external pressure mounted. The full account of this relationship is detailed in the explanation of how the ISI built and protected the world’s most dangerous militant groups.

The Pakistan Army’s institutional posture toward the seminary network has been more ambivalent than the ISI’s, varying with the personalities of senior officers and the strategic priorities of the moment. Some army chiefs have made genuine efforts to disrupt elements of the militant infrastructure, particularly when the parent organisations have begun targeting the Pakistani state itself rather than only Indian targets. General Ashfaq Parvez Kayani, who served as army chief from 2007 to 2013, oversaw operations against Tehrik-i-Taliban Pakistan after that organisation’s domestic attacks intensified, but the army’s posture toward the India-focused groups, LeT and JeM, remained markedly different. The institutional logic was that the India-focused groups, whatever their externalities, served Pakistani strategic interests by tying down Indian forces in Kashmir and by maintaining the deniable second front that Pakistan’s conventional military lacked the capability to maintain through state-to-state confrontation. Senior officers who shared this institutional logic, regardless of personal religious orientation, treated the India-focused seminaries as strategic assets to be protected rather than threats to be neutralised.

The civilian political class has been similarly ambivalent and similarly variable. Civilian governments have periodically committed to seminary regulation, particularly when international pressure has intensified. The Musharraf government’s 2003 Madrasah Reform Project, which aimed to require seminary registration and curriculum modernisation, foundered on clerical resistance and was effectively abandoned within two years. The Sharif government’s post-2014 commitments under the National Action Plan, formulated after the December 2014 Peshawar Army Public School attack that killed more than 130 children, included madrassa registration as one of its twenty points but produced limited substantive change. The Imran Khan government’s 2019 reclassification of seminaries as educational institutions under the Ministry of Education, with the creation of the Directorate General of Religious Education, was undertaken under direct FATF pressure and similarly produced more procedural change than substantive transformation. Each successive reform initiative has confronted the same political obstacle: the seminary network has electoral allies, including the Jamiat Ulema-e-Islam Fazl and Jamaat-e-Islami parties, whose mobilisation capacity makes sustained confrontation costly for any government that attempts it.

The Pakistani religious establishment beyond the militant networks has also functioned as a protective layer. When the Pakistani government has attempted regulation, the response has typically been framed not as defence of specific militant networks but as defence of religious autonomy from secular state intrusion. The 2024 Societies Registration Amendment Bill, which would have shifted seminary oversight back from the education department to deputy commissioners, drew opposition from religious lobbies that framed the legislation as undermining the ideological character of the country. Similar patterns have repeated across regulatory efforts. The militant networks themselves rarely lead the public opposition to regulation. The opposition is led by ostensibly mainstream religious figures whose own institutions are not implicated in militancy but who frame regulation of any seminary as an existential threat to all seminaries. The militant networks benefit from this framing without having to make their own case publicly.

The protection extends to specific individuals when international pressure mounts against them. Hafiz Saeed has been arrested multiple times in his career, including periods of house arrest after 2008 and convictions on terror financing charges in 2020. Each detention has been followed by partial restoration of his operational position, even when formal release has been delayed. The seminary network has continued operating throughout these detentions, in some cases under the formal control of his family members, in other cases under interim leadership that defers to him on substantive decisions. Masood Azhar’s status has been even more anomalous. After being released in the IC-814 hostage exchange in December 1999, the JeM founder has periodically been described by Pakistani officials as detained, missing, or otherwise unavailable, with the actual status of his physical custody being something Pakistani authorities have declined to clarify. This ambiguity itself is protection. So long as Pakistan can claim that Azhar is detained, the international community has reduced incentive to press further. So long as Azhar can issue communications through his network, the operational system continues to function.

The protective infrastructure also includes specific judicial and procedural mechanisms. Anti-terrorism cases against seminary administrators frequently fail in Pakistani courts because witnesses fail to appear, evidence is mishandled, or prosecutors withdraw charges under various pressures. Convictions, when they occur, are often on financial offences rather than the underlying militant activity. Sentences are often suspended or commuted. The cumulative effect is a justice system in which the seminary administrators face limited consequences for their institutional roles, even in the rare cases where prosecution is undertaken at all. The pattern has been documented in successive State Department reports on Pakistan and in FATF mutual evaluations during the 2018 to 2022 grey-listing period.

What this state sponsorship and protection means for the prospect of dismantling the pipeline is sobering. A pipeline embedded in protective state and religious infrastructure cannot be eliminated by external pressure alone. The pipeline can be reduced. The pipeline can be made costlier to operate. Specific institutions can be closed, specific administrators arrested, specific funding streams interrupted. But the institutional ecosystem that produces the pipeline reproduces the pipeline because the underlying calculations have not changed. The Pakistani security establishment continues to view the India-focused seminaries as strategic assets. The Pakistani religious establishment continues to view seminary regulation as illegitimate state intrusion. The Pakistani political class continues to find it electorally costly to confront the religious lobby. Until these underlying conditions shift, the pipeline will continue to operate.

International Designation and Sanctions

The international community has imposed multiple layers of designation and sanction on the principal organisations that operate the militant pipeline, and the results offer a useful test of how effectively external pressure can disrupt the seminary infrastructure when the host state is not cooperating in good faith. The record is mixed but instructive.

LeT was designated by the United States as a Foreign Terrorist Organisation in December 2001, by the United Nations Security Council 1267 sanctions committee in May 2005, and by the European Union and Canada around the same period. JuD, the principal seminary front, was designated by the UN in December 2008 following the 26/11 Mumbai attacks, and by the United States Treasury Department around the same period. Falah-i-Insaniyat Foundation, the secondary front to which JuD’s operations partially migrated, was designated by the United States Treasury in November 2010 and by the UN in March 2012. JeM was designated by the United States in December 2001 and by the UN in October 2001, with Masood Azhar himself finally added to the UN 1267 list in May 2019 after years of Chinese vetoes that had previously blocked the designation. These designations carry specific legal consequences: asset freezes, travel bans, prohibitions on financial transactions with the designated entities, and obligations on UN member states to enforce these measures domestically.

The actual effect of these designations on the seminary network has been considerably less than the legal architecture would suggest. The principal reason is that the designations apply to specific named entities, while the seminary infrastructure can be repackaged under new names that are not yet designated. When JuD was sanctioned in 2008, its operations migrated partially to Falah-i-Insaniyat Foundation. When that organisation was sanctioned, operations migrated to other shell entities. The seminary buildings remained the same. The personnel remained the same. The students remained the same. The funding flows were rerouted through new organisational identities that took months or years to track and designate. Each successive designation imposed temporary disruption but not permanent dismantling.

The Financial Action Task Force grey-listing of Pakistan from 2018 to 2022 represented the most systematic external pressure ever applied to the seminary infrastructure. FATF placed Pakistan on its grey list of jurisdictions with strategic anti-money-laundering and counter-terrorism-financing deficiencies in June 2018 and required Pakistan to complete a forty-point action plan as a condition for removal. Several action items related directly to the seminaries: requirements for transparent registration of religious institutions, requirements for financial oversight of seminary fundraising, and requirements for prosecution of designated entities operating under shell names. Pakistan’s progress against these action items was the subject of ongoing review at successive FATF plenary meetings, with the country’s grey-list status repeatedly extended as analysts assessed the substantive impact of stated reforms.

Pakistan was removed from the FATF grey list in October 2022 after completing the action plan to FATF’s stated satisfaction. The removal was the formal closure of the grey-listing episode but the substantive impact on the seminary network was subject to continuing debate. The reform initiatives that Pakistan had completed during the grey-listing period included the 2019 reclassification of seminaries under the Ministry of Education and the establishment of the Directorate General of Religious Education. The reform initiatives also included some prosecution of designated entities and some interruption of identifiable financial flows. But the militant pipeline itself, the structural mechanism by which JuD and JeM seminaries continue producing recruits, was not fundamentally disrupted by the FATF process. The seminaries that had been reclassified continued operating. The personnel who had been administering the seminaries continued in their positions. The students continued enrolling. The graduates continued moving into the operational ranks of the parent organisations.

The reform process did however produce one substantive change: the seminaries became more difficult to operate openly. The pre-2018 pattern, in which JuD operated approximately three hundred seminaries across Pakistan with public branding and visible administrative offices, was replaced by a more dispersed and discreet model in which the same seminaries operated under various reformed identities with reduced public visibility. The change is meaningful for international monitoring purposes. It is less meaningful for the actual functioning of the pipeline. A seminary that has changed its public identity but retained its physical campus, its personnel, and its student body has not been disrupted in any operationally significant way.

The continuing inadequacy of the international response reflects a structural feature of the sanctions architecture. Sanctions work best against entities whose principal vulnerability is access to the international financial system. They work less well against entities whose principal funding comes from domestic informal channels, whose principal personnel are in jurisdictions that do not enforce sanctions reliably, and whose principal physical assets are in territories beyond the reach of sanctioning states. The seminary infrastructure has all three of these characteristics. It is funded primarily through hide collection, donation boxes, and hawala flows that never touch the international financial system. Its personnel are in Pakistan, where enforcement depends on Pakistani political will. Its physical assets are in Pakistani cities where seizure requires Pakistani state action. The sanctions architecture, however well-designed for other purposes, was not designed for an adversary structured like the militant pipeline.

The lesson of the international response is that external pressure is necessary but not sufficient. External pressure has imposed real costs on the seminary network, has disrupted some specific operational nodes, and has accelerated some Pakistani regulatory actions that might not otherwise have occurred. But external pressure cannot substitute for sustained domestic Pakistani action against the seminary infrastructure, and that domestic action has not been forthcoming because the Pakistani institutions whose action is required, the security establishment most centrally, continue to view the pipeline as a strategic asset. Until that strategic calculation shifts within Pakistan, no external sanctions architecture will produce the structural transformation the seminaries would require.

The Targeted Elimination Campaign

The shadow war’s engagement with the militant pipeline has been indirect rather than direct. The unknown gunmen who have eliminated dozens of Pakistan-based militants since 2020 have not, with rare exceptions, targeted the seminaries themselves. Bombings of seminary buildings, killings of teachers, raids on educational facilities, these are not the patterns the campaign has produced. What the campaign has done instead is target individuals whose roles connect operational fighters to the seminary infrastructure that produced them. The pattern is selective and revealing.

Sardar Hussain Arain was killed near his shop in Nawabshah, Sindh, in early 2023 by motorcycle-borne assailants who escaped without identification. Arain’s name had appeared in Indian intelligence assessments as a JuD operative responsible for managing the organisation’s seminary infrastructure across the lower Sindh districts. He was not a senior LeT commander. He was not personally connected to any specific terror attack against Indian targets. His operational role was administrative: identifying potential recruits in his region, managing the relationships between village seminaries and the regional flagship institutions, channeling funds through the Sindh charitable network, coordinating with JuD’s central leadership on policy implementation in his districts. His killing, when it came, was striking because it suggested that the targeting cycle had begun reaching into the recruitment apparatus rather than only the operational ranks. The full account is documented in the profile of the JuD operative killed in Nawabshah.

Syed Noor Shalobar was killed in Khyber Pakhtunkhwa in March 2023 in similar circumstances. Shalobar’s role had been documented in Indian intelligence assessments as a recruiter who worked with both Pakistan Army and ISI personnel to identify Kashmiri youth for radicalisation and infiltration. The seminary network was central to Shalobar’s recruitment work. He maintained relationships with senior figures in seminaries across KPK and the southern districts of Punjab, identifying students whose religious profile and operational potential matched the parent organisations’ intake criteria. His elimination, like Arain’s, signaled that the campaign was reaching beyond the fighters and into the structural connections between the seminaries and the operational network. The full background is set out in the profile of Shalobar’s KPK recruitment work.

The pattern of targeting administrators and recruiters rather than seminary buildings or teachers reflects a specific operational logic. Eliminating a seminary building accomplishes little. Another building can be constructed, often within months. Eliminating a teacher accomplishes little. Another teacher can be hired, often within weeks. Eliminating an administrator who maintained the connections between multiple institutions and the parent organisation accomplishes more, because the administrator’s accumulated relationships, contextual knowledge, and personal trust networks are not transferable. A successor can take the title and the office, but the successor cannot inherit the operational fluency that the eliminated administrator had built across years. Each such elimination imposes a temporary delay on the relevant function while the parent organisation reconstitutes its capacity.

The cumulative effect of these targeted eliminations on the pipeline as a whole is, however, modest. The seminaries continue to enrol students. The students continue to advance through the conditioning and preparation stages. The graduates continue to be available for handoff to the parent organisations’ military training infrastructure. The administrators who have been eliminated represent a small fraction of the personnel who staff the pipeline at any given moment, and the parent organisations have surplus capacity to absorb the losses without operational disruption. The pipeline is not, by the structure of its design, vulnerable to attrition through individual eliminations alone. Disrupting the pipeline at structural level would require either the closure of the principal physical campuses, including Markaz-e-Taiba in Muridke and the Bahawalpur facilities, or the systematic disruption of the financial flows that sustain the seminaries’ day-to-day operations. The shadow war, by its nature, can do neither.

What the shadow war can do, and has begun to do, is alter the calculations of the individuals who staff the pipeline. An administrator who knows that previous administrators in his region have been killed during their daily routines must reconsider the calculus of his own visibility. He may move more cautiously, vary his routes, reduce his public profile, sacrifice some operational efficiency for personal security. The cumulative effect of these individual adjustments is a slower and more expensive pipeline. Recruits move through the system somewhat more slowly because the administrators who would otherwise process them are operating with reduced capacity. Funds flow somewhat more slowly because the personnel who would otherwise move them are operating with greater caution. The pipeline continues to function, but at lower throughput. This effect, accumulated across many cases, is real and measurable, even if it falls well short of structural disruption.

The connection between the targeted killings and the seminary network reveals something else important about the shadow war’s intelligence base. To eliminate Arain in Nawabshah, the operating cell needed to know which person in Sindh was managing JuD’s regional seminary infrastructure. This is not information available from public reporting. This is information available only to intelligence services with deep penetration of the JuD organisational structure. The same logic applies to Shalobar’s elimination, where the relevant question is which person in KPK was managing the recruitment relationships with the Pakistan Army. The fact that these eliminations have been carried out at all suggests intelligence access of remarkable depth. Either Indian intelligence has placed assets within the seminary network itself, or has acquired the relevant personnel data through intercepted communications, or both. The seminary network’s institutional opacity, which had been one of its principal protections, is no longer absolute.

The shadow war’s relationship with the pipeline thus operates at three distinct levels. At the level of individual eliminations, the campaign has begun reaching into the recruitment infrastructure but is far from systematically dismantling it. At the level of operational throughput, the campaign has imposed measurable but modest costs on the pipeline’s productive capacity. At the level of strategic signaling, the campaign has demonstrated that the seminary network’s personnel are not beyond the reach of intelligence services that wish to find them. Each level matters. The first level alone is insufficient to dismantle the pipeline. The second level alone is insufficient to materially degrade the parent organisations. The third level, however, may be the most consequential of the three. A seminary administrator who has come to believe that he can be found, identified, and killed during his ordinary routine has reached a different mental state than an administrator who believed himself invisible. The accumulation of such mental shifts across the network reshapes the operational culture in ways that go beyond what any specific elimination would imply on its own.

Current Status and Future Trajectory

The militant pipeline is, as of the present moment, simultaneously under more sustained pressure than it has ever faced and more institutionally durable than international observers tend to recognise. Both observations are accurate. The pipeline is being squeezed. The pipeline is also surviving the squeeze. The future trajectory depends on which of these forces, the squeeze or the survival, accelerates.

The pressure has multiple sources, each significant. The Indian shadow war has begun reaching the recruitment apparatus, as documented above. The Indian conventional response has begun reaching the seminary buildings themselves, with Operation Sindoor’s targeting of Bahawalpur in May 2025 representing the most significant kinetic strike against JeM’s institutional infrastructure since the 2019 Balakot strikes. The Pakistani state has implemented some level of regulatory reform under FATF pressure, even when the substantive effect has been limited. International designations have continued to expand, with Masood Azhar’s 2019 UN listing closing one of the principal gaps in the legal architecture. Western governments have accumulated additional intelligence on the network’s funding flows and personnel deployments through years of monitoring. The pipeline operates today in a more constrained environment than it did a decade ago.

The institutional durability is also real and structural. The seminary buildings remain in place. The Muridke campus continues operating, with its two-hundred-acre complex servicing students from across Punjab and beyond. The Bahawalpur facilities, despite the Operation Sindoor strike, have shown the resilience characteristic of the network’s institutional architecture, with rapid rebuilding and continued enrolment after the strike. The funding mechanisms remain functional. Hide collection continues each Eid-ul-Adha. Donation boxes remain in markets across the seminary catchment areas. Hawala flows continue moving funds outside the formal financial system. The personnel remain available. Students continue enrolling. Teachers continue teaching. Administrators continue managing relationships. Recruits continue advancing through the four-stage conversion process.

The honest assessment is that the pipeline is being constrained but is not collapsing. Throughput is somewhat lower than it would be without the pressure, but throughput remains adequate to replace the operational losses that the parent organisations have suffered through the targeted killings. The parent organisations have lost senior figures, including key targets like Shahid Latif killed in Sialkot and others profiled in the broader campaign, but the seminaries continue to produce successors capable of taking up the operational positions vacated by elimination. The replacement is not perfect. The successors typically have less experience than the eliminated figures. The institutional knowledge built up across decades cannot be transferred fully to a younger generation in the timeframes the parent organisations are working with. There is degradation in operational quality. But the degradation is gradual rather than catastrophic.

The question for the next several years is whether the pressure will accelerate or stabilise. Several scenarios are plausible. In the most pessimistic scenario, from the Indian standpoint, the current pressure stabilises at a level that the pipeline has demonstrated it can absorb. The seminaries continue producing recruits at slightly reduced rates. The parent organisations continue replacing their losses. The shadow war continues eliminating individual operatives without disrupting the institutional architecture that produces them. This scenario would mean a long-running attritional confrontation in which neither side achieves decisive results, a confrontation that could continue for decades without resolution. In the most optimistic scenario, from the Indian standpoint, the cumulative pressure crosses a threshold at which the parent organisations can no longer maintain operational quality despite the seminary network’s continued throughput. This would manifest as more frequent operational failures, more interceptions of infiltration attempts, more disruption of attack planning, and a general decline in the parent organisations’ ability to project meaningful threat. The pipeline would still operate, but its outputs would no longer be operationally consequential.

A third scenario, lying between these, may be most likely. The pressure continues to accumulate, the parent organisations continue to adapt, and the equilibrium shifts gradually toward Indian advantage without ever producing decisive collapse of the pipeline. This scenario would mean continued shadow war eliminations, continued seminary operations, continued occasional attacks by parent organisation operatives, and continued geopolitical confrontation between India and Pakistan over the seminary infrastructure. The status quo would persist, but the relative balance within the status quo would shift.

What would be required to produce structural disruption of the pipeline rather than continued attritional confrontation is something that no party currently has the capability or political will to provide. It would require sustained Pakistani action against the seminary network of a kind that the Pakistani state has shown no inclination to undertake. It would require the Pakistani security establishment to recognise that the long-term costs of maintaining the pipeline now exceed the strategic benefits, a calculation that the security establishment has so far refused to make. It would require Pakistani civilian governments to confront the religious lobby in ways that no civilian government has been politically willing to do. The structural disruption that would actually dismantle the pipeline depends on a Pakistani transformation that is currently nowhere visible on the political horizon.

In the absence of that transformation, the pipeline will continue to operate. The shadow war will continue to constrain it. The seminaries will continue to produce recruits. The parent organisations will continue to deploy them. The cycle that began in the 1980s, when the seminaries were repurposed for jihad against the Soviets and then for jihad against India, will continue into a future that, on present evidence, is closer to the past than to any decisive break from it. The pattern that the shadow war has documented is real. The pattern’s limits are equally real. Both must be held in view simultaneously to understand what the campaign is actually achieving and what would be required to achieve more.

The hopeful note, such as it is, lies in the long arc rather than the immediate horizon. Pipelines like the Pakistani militant infrastructure do not last forever. Empires that built them have fallen. Doctrines that justified them have eroded. Generations that staffed them have aged out. The Saudi state that once funded the seminary network has shifted its religious export programme. The Pakistani state that once viewed the seminaries as strategic assets has begun to confront the costs as the operational fighters have turned their guns inward. The pipeline that has produced four decades of fighters is not a permanent feature of South Asian geopolitics. It is a contingent institutional arrangement that will eventually unravel as its conditions of possibility erode. The question is not whether the unraveling will occur but how long it will take and how many additional Indian deaths it will cost in the meantime. The shadow war is one mechanism among several that may shorten the timeline. It is not the only mechanism. It cannot be the only mechanism. The unravelling, when it comes, will be the work of forces larger than any single campaign.

Frequently Asked Questions

Q: How do Pakistani madrassas recruit for terror groups?

The recruitment is sociological rather than ideological in its initial stage. Seminaries operated by JuD, JeM, and allied networks identify potential recruits primarily through poverty, where rural families lacking the means for secular education send their sons because the seminary provides free room, board, and instruction. Once enroled, the boy spends years in religious study, with political content introduced gradually starting around age twelve and intensifying through adolescence. By age sixteen or seventeen, the seminary administrators have selected boys who show religious aptitude and ideological commitment for further development. These selected boys are introduced to the parent organisation’s senior figures, attend specialised study programmes that include physical conditioning alongside religious instruction, and eventually transition to formal military training under the parent organisation’s command. The conversion is graduated across multiple years rather than abrupt at any single moment, which is why family interventions to retrieve sons mid-pipeline often fail. The boy by that stage has internalised the seminary’s ideological frame as his own personal religious certainty.

Q: Are all madrassas in Pakistan extremist?

No, and the question itself is part of why the seminary system has proven so resistant to reform. Pakistan has somewhere between 30,000 and 40,000 seminaries depending on which counting methodology is applied, with the official 2023 economic survey identifying 36,331 institutions. Most of these are doctrinally conservative but politically inert, providing religious education to families who have no alternative without producing operational fighters for any organisation. Estimates from the early 2000s suggested that ten to fifteen percent of Pakistani seminaries promote extremist ideologies of the kind that supplies recruitment to LeT, JeM, and similar networks. The blanket characterisation of the entire system as a militant pipeline is inaccurate and politically counterproductive, because it provides cover for the genuinely problematic subset by allowing defenders to point to the broader system. The accurate analysis distinguishes the militant subset from the broader system, identifies which specific schools and which specific seminary networks produce fighters, and addresses the militant subset on its own terms without conflating it with seminaries that perform legitimate educational functions.

Q: How many madrassas does JuD operate?

At the peak of its registered presence, JuD operated approximately three hundred seminaries across Pakistan, with concentrations in Punjab and Sindh and a smaller footprint in Khyber Pakhtunkhwa. The figure has fluctuated since 2018 as Pakistan responded to FATF pressure with various reform measures including reclassification of seminaries under the Ministry of Education and the establishment of the Directorate General of Religious Education. The number of seminaries operating under the JuD brand or its successor identities has decreased somewhat under this pressure, but the actual number of seminaries operating under JuD’s effective control, regardless of formal branding, has decreased less. Many of the seminaries that no longer carry the JuD identity continue to be staffed by personnel previously affiliated with the organisation, continue to teach the curriculum the organisation developed, and continue to feed recruits into the parent terror group’s military training infrastructure. Counting institutions by formal affiliation rather than by functional connection significantly understates the network’s actual scope.

Q: What is taught in JeM-affiliated madrassas?

The curriculum in JeM-affiliated seminaries combines standard Deobandi religious instruction with specific texts authored by Masood Azhar and his close associates that frame jihad as an ongoing personal obligation incumbent on every adult male Muslim. Azhar’s published works including “Fazail-e-Jihad” articulate this doctrine systematically. Students study the Quran and hadith as in any Deobandi seminary, but they study them through interpretive frames that treat selective passages emphasising armed conflict as the doctrinally privileged readings. They study Islamic history with emphasis on military conquests and on episodes of Muslim defeat that the curriculum frames as religious failures requiring rectification. They study contemporary geopolitics through the lens of an enduring conflict between Muslim communities and external powers, with India occupying a particularly prominent place in the geographic frame. The political and historical content is integrated with the religious content rather than presented as a separate addendum, which makes the doctrine harder to identify and disrupt because individual passages of instruction look superficially indistinguishable from non-militant Deobandi seminary content.

Q: How long does radicalisation take in a madrassa?

The full conversion from a nine-year-old village student to an operationally deployable fighter typically takes between ten and thirteen years, divided across the four stages described above. Stage one, basic religious enrolment, runs from approximately age eight to age twelve. Stage two, conditioning at a regional seminary, runs from approximately age twelve to age sixteen. Stage three, preparation at an institutional centre, runs from approximately age sixteen to age nineteen. Stage four, handoff to the parent organisation’s military training, occurs at approximately age nineteen to age twenty-one, with the recruit typically becoming operationally deployable around age twenty-two. Some recruits move through the pipeline more quickly when they are recruited at older ages or when their backgrounds make extended preparation unnecessary. Some take longer when family circumstances or personal hesitation slow the conversion. But the overall timeframe of roughly a decade from enrolment to deployment is consistent across documented cases. The long timeframe is itself a feature of the system. It produces fighters whose ideological commitment is internalised over years, who do not experience the conversion as imposed, and who consequently are more reliable than recruits who have undergone briefer indoctrination programmes.

Q: Can the madrassa pipeline be shut down?

It can be disrupted in stages, but a complete shutdown would require sustained Pakistani state action of a kind that has not been forthcoming and that current political conditions do not make likely. The disruption that has been achieved through international pressure, FATF grey-listing, targeted designations, and sanctions has imposed real costs on the seminary network without dismantling its institutional architecture. The disruption that would be achieved through more sustained Pakistani action, comprehensive registration with effective enforcement, prosecution of seminary administrators with linkage to designated organisations, interruption of the financial flows that sustain the seminaries, and replacement of the educational vacuum the seminaries fill with credible state-provided alternatives, would be qualitatively different but is not currently being undertaken. The pipeline has survived four decades because the conditions that allowed it to grow have not yet been altered. Until those conditions are altered, the pipeline will continue to function in some form even if its specific institutional manifestations change.

Q: Why do families send children to militant-linked madrassas?

The principal reason is poverty rather than ideology. Families in southern Punjab, rural Sindh, and Khyber Pakhtunkhwa face an educational choice in which the alternatives to seminary enrolment are either nonexistent or unaffordable. Government schools in these regions are often understaffed, underresourced, and effectively non-functional. Private secular schools require tuition that families cannot pay. The seminary, by contrast, provides free room, free board, free instruction, and the prospect of a religious vocation that gives the boy social standing he could not otherwise achieve. For families weighing these options, the seminary is the rational choice on educational and economic grounds. The fact that some seminaries are linked to militant organisations is not visible to families at the point of enrolment, because the militant linkages are not advertised at the village feeder level. Families who would be reluctant to send sons to known militant seminaries are nonetheless willing to send them to local seminaries that, unbeknownst to the families, function as feeders for the regional flagships connected to the parent organisations.

Q: Does the Pakistani government regulate madrassa content?

Pakistani regulatory efforts have been recurrent but ineffective. Successive governments since the 1960s have launched seminary reform initiatives, beginning with the Ayub Khan era, continuing through the Musharraf government’s 2003 Madrasah Reform Project, and most recently through the Imran Khan government’s 2019 reclassification under the Ministry of Education. Each initiative has produced procedural change including registration requirements, curriculum guidelines, and oversight mechanisms, but each has been blunted by clerical resistance, by political opposition from the religious lobby, and by inadequate enforcement capacity even when laws have been passed. The post-2014 National Action Plan, which followed the Peshawar Army Public School attack that killed more than 130 children, included madrassa registration as one of its twenty action items, but the substantive implementation against the militant-affiliated subset has been limited. The pattern is not one of complete regulatory absence but of regulation that is announced periodically, partially implemented, and rarely sustained against the seminaries that most need oversight.

Q: Which Pakistani schools of Islamic thought produce the most militant recruits?

The Deobandi and Ahl-e-Hadith schools provide the overwhelming majority of recruits to the principal anti-India militant networks. The JeM pipeline draws from Deobandi seminaries, particularly those connected to the Banuri Town complex in Karachi and the Bahawalpur institutional centre. The LeT pipeline draws from Ahl-e-Hadith seminaries, particularly those affiliated with the Markaz Dawat-ul-Irshad and its successor identities. Together these two schools account for less than fifteen percent of all Pakistani seminaries by registration but for approximately ninety percent of the recruits who enter the militant pipeline. The Barelvi school, which represents about a quarter of registered seminaries, produces almost no recruits to the principal anti-India militant networks because Barelvi doctrine venerates saints and shrines that the Deobandi and Ahl-e-Hadith strands consider polytheistic. This sectarian dimension matters for any analysis of the pipeline because it identifies which subset of the broader seminary system actually feeds militancy and which subsets do not.

Q: How is the militant pipeline funded?

Funding flows through three principal streams. Domestic charitable collection, including hide donations during Eid-ul-Adha, donation boxes in markets and bus terminals, and door-to-door drives during Ramadan, provides the largest share. Foreign donations, historically dominated by Saudi and Gulf state contributions but also including Pakistani diaspora funding through hawala networks, provide the second stream. State subsidy, through Auqaf department disbursements, tax exemptions on charitable activity, and concessional provision of utilities and land, provides the third. The streams are difficult to disrupt because each operates outside the formal financial system that international counter-terror finance tools are designed to monitor. The hide collection occurs once a year through volunteer networks. The donation boxes operate continuously through cash transactions. The hawala flows leave no banking trail. The state subsidies are politically protected by the religious lobby’s electoral mobilisation capacity. Disrupting any single stream is difficult. Disrupting all three is what would actually impair the pipeline.

Q: Has international pressure reduced the militant pipeline’s capacity?

The pressure has produced measurable reductions in the pipeline’s operating margin without producing structural disruption. FATF grey-listing of Pakistan from 2018 to 2022 forced the implementation of registration requirements and oversight mechanisms that did interrupt some funding flows and did make open public operation of the seminary network more difficult. International designations of LeT, JuD, JeM, and senior figures including Hafiz Saeed and Masood Azhar have produced asset freezes and travel bans that have constrained the principal organisations’ international operations. Western intelligence cooperation has accumulated information that has supported the targeted killings now reaching into the recruitment apparatus. Each of these forms of pressure has imposed real costs. None of them has produced the structural transformation that would actually dismantle the pipeline. The seminaries continue operating. The students continue enrolling. The recruits continue advancing through the conversion stages. The parent organisations continue receiving the outputs. The international pressure has constrained the system without breaking it.

Q: What role do Saudi-funded networks play in Pakistani militancy?

Saudi funding played a central role in expanding the seminary network during the 1980s and 1990s, both through formal Saudi governmental and royal-family charity foundations and through informal networks of private Saudi donors. The 9/11 Commission report documented this funding’s role in the broader emergence of jihadist networks across the region. Saudi government policy has shifted significantly since 2017 under Crown Prince Mohammed bin Salman, with the kingdom publicly distancing itself from religious export programmes and reducing official support for seminary expansion abroad. The historical infrastructure that the Saudi flows built remains in place, however, and private donors with personal sympathies have continued some level of contribution outside the official channels. The Saudi role today is therefore considerably reduced compared to its 1980s peak but is not zero, and the institutional patterns that the Saudi funding established continue shaping the seminary network even when the funding itself has been redirected. The relationship illustrates a broader pattern: external sponsorship that built jihadist institutions over decades cannot be unbuilt simply by withdrawing the funding, because the institutions have developed their own funding and reproduction mechanisms in the meantime.

Q: Are Indian Muslims being recruited through the Pakistani pipeline?

The principal pipeline produces recruits primarily from rural Pakistani populations, especially in southern Punjab, Sindh, and Khyber Pakhtunkhwa. The recruitment of Indian Muslims is a separate channel managed through different mechanisms, principally through indoctrination of vulnerable individuals over digital platforms, through the activities of Indian-side facilitators who serve as recruiters for Pakistan-based handlers, and through the relatively small numbers of Indian nationals who travel to Pakistan, are radicalised in seminaries there, and return to operate as cells within India. The numbers involved in this Indian-side recruitment are small in absolute terms relative to the Pakistani pipeline, but the Indian recruits play disproportionate operational roles because their movement within India does not trigger the immigration alerts that would identify Pakistani fighters crossing the border. The Pakistani seminary pipeline and the Indian-side radicalisation channel are linked, with Pakistani-trained handlers managing the Indian recruits, but they are operationally distinct flows that require different countermeasures.

Q: How does Pakistan’s military view the seminary network?

The Pakistani military’s institutional posture has been ambivalent and has shifted across periods. During the 1980s under Zia-ul-Haq, the military actively built the seminary network as part of the Afghan jihad mobilisation. During the 1990s, the military redirected the seminary outputs from Afghanistan to Kashmir, with ISI’s S-Wing maintaining close liaison with LeT and JeM. During the 2000s under Musharraf, the military’s posture became more complicated, with operations against some militant networks while the India-focused groups continued to receive institutional protection. During the 2010s and 2020s, the military has launched operations against Tehrik-i-Taliban Pakistan and associated domestic threats while continuing to view the India-focused seminary networks as strategic assets. Senior officers vary in their personal assessments. Some have advocated more comprehensive action against all militant networks. Others have continued to view differential treatment of India-focused versus domestically-focused groups as strategically rational. The institutional posture is therefore not monolithic but reflects the unresolved internal debate within the security establishment about whether the militant assets continue to provide net strategic benefits.

Q: What happens to seminary graduates who do not become fighters?

Most seminary graduates do not become operational fighters even within the militant-affiliated networks. The pipeline is selective at every stage, with the majority of students at each level being graduated rather than advanced. These graduates typically return to their home villages and serve as local clerics, mosque imams, or seminary teachers in the next generation of village feeder institutions. This pattern is significant for two reasons. First, it means the seminary networks have a much larger social footprint than the operational fighter count would suggest, with thousands of village clerics and teachers across Pakistan whose education was shaped by the militant pipeline even when they themselves did not advance through it. Second, it means the pipeline reproduces itself through both its successes and its rejections, with rejected candidates becoming the next generation of village teachers who identify and recommend students for the same pipeline that processed them. The graduate who became a village imam rather than a Kashmir infiltrator is nonetheless an asset of the broader network, both as a community presence and as a recruiter for future cohorts.

Q: Can targeted killings disrupt the seminary infrastructure?

Targeted killings have begun reaching into the recruitment apparatus, as the eliminations of Sardar Hussain Arain in Nawabshah and Syed Noor Shalobar in KPK demonstrate, but the structural impact on the pipeline has been modest. Eliminating individual administrators and recruiters imposes temporary delays as the parent organisations replace the personnel, but the seminaries themselves continue operating, the students continue enroling, and the conversion process continues advancing through its stages. Disrupting the pipeline at structural level would require either closure of the principal physical campuses, including Markaz-e-Taiba in Muridke and the Bahawalpur facilities, or systematic interruption of the financial flows that sustain the seminaries’ day-to-day operations. The targeted killings, by their nature, can do neither. What they can do is alter the calculations of the personnel who staff the pipeline, making them more cautious in their movements and slower in their work. The cumulative effect of these adjustments is real but incremental. Structural transformation of the pipeline depends on Pakistani state action, not on the pace of individual eliminations.

Q: Why have Pakistani reform efforts failed to dismantle the militant pipeline?

The reforms have failed because they have addressed the symptoms rather than the underlying conditions. Registration requirements have been imposed but enforcement has been selective, with the militant-affiliated seminaries often finding ways to comply formally while continuing operations substantively. Curriculum oversight has been mandated but inspection has been limited, with seminaries continuing to teach the militant content while presenting reformed curricula for official review. Financial transparency has been required but the principal funding streams operate through informal channels that the formal financial system cannot monitor. Each of these reform mechanisms could in principle have meaningful impact if backed by political will and enforcement capacity. Both have been lacking. The political will is absent because the religious lobby’s electoral mobilisation capacity makes sustained confrontation costly for any government. The enforcement capacity is absent because the security establishment has not committed to the kind of comprehensive action against the militant networks that would be required. Until both shift, the reforms will continue producing announcements without producing transformation.

Q: What would actually shut down the militant seminary network?

A genuine shutdown would require simultaneous action across four dimensions. First, the educational vacuum the seminaries fill would have to be filled with credible state-provided alternatives. This means functional government schools in southern Punjab, rural Sindh, and KPK with adequate teachers, textbooks, and infrastructure. Second, the institutional centres of the militant networks, including Markaz-e-Taiba in Muridke and the JeM Bahawalpur complex, would have to be physically closed and the personnel arrested or relocated. Third, the financial flows that sustain the seminaries would have to be systematically interrupted across all three major streams, domestic collection, foreign donations, and state subsidy. Fourth, the Pakistani security establishment would have to commit institutional support to the shutdown rather than passive obstruction. None of these four conditions currently obtains. None is likely to obtain in the near term. The combination of all four would require Pakistani political and institutional transformation of a kind that has not occurred in the four decades since the pipeline was constructed and that current political conditions provide no clear path toward producing.

Q: How does the Pakistani militant seminary system compare to other militant infrastructure globally?

Among contemporary militant educational infrastructures, the Pakistani system is unusual in three respects. First, it operates within a nominally allied state that has formal counter-terrorism cooperation with Western governments, which constrains the kinds of pressure that can be applied. Second, it produces fighters at a scale, several thousand per year across the principal networks, that is larger than most contemporary jihadist recruitment infrastructures. Third, it has institutional durability across more than four decades, surviving Soviet withdrawal from Afghanistan, the post-9/11 international counter-terror campaign, two periods of FATF grey-listing for Pakistan, and ongoing targeted operations against its operational outputs. Comparable infrastructures historically have included the Taliban-aligned seminary network in Afghanistan during the 1990s, certain Salafi seminary networks in Yemen and Saudi Arabia during particular periods, and elements of the Iranian Revolutionary Guard Corps’ clerical recruitment apparatus. None of these has demonstrated the same combination of state cover, institutional scale, and temporal durability as the Pakistani case. The Pakistani militant pipeline is, by these measures, the most institutionally entrenched jihadist recruitment infrastructure currently operating anywhere in the world.

Q: What is the long-term outlook for the militant pipeline?

The long-term outlook depends on shifts that are larger than any current campaign. The Saudi state’s withdrawal from religious export programmes is one such shift, removing one of the principal historical funding sources. The Pakistani state’s gradual confrontation with domestic militant networks that have turned against it is another, eroding the institutional logic that justified maintaining the broader system. The international community’s growing intolerance for state-sponsored proxy warfare is a third, raising the diplomatic costs of continuing the current arrangement. None of these shifts is sufficient on its own to dismantle the pipeline. Together, over decades rather than years, they may erode the conditions that sustain it. The pipeline that has produced four decades of fighters is not a permanent feature of South Asian geopolitics. It is a contingent institutional arrangement that will eventually unravel as its conditions of possibility erode. The shadow war is one mechanism among several that may shorten the unraveling timeline. It is not the only mechanism. The full unraveling, when it comes, will be the work of forces larger than any single campaign and longer than any current observer’s strategic horizon.