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Pakistan was established in 1947 as a homeland for South Asia’s Muslims following the end of British colonial rule on the Indian Subcontinent. The majority of Pakistanis practice a moderate form of Sufi Islam, but Islamist political parties exercise significant influence within society and through the courts, as well as help shape political debates, foreign policy, and the development of legislation. Moreover, throughout Pakistan’s history, its military and intelligence services have created and cultivated ties with violent Islamist groups to achieve regional strategic objectives. The U.S. war in Afghanistan following the September 11, 2001 terrorist attacks, and Pakistan’s role in fighting terrorism in recent years, has severely complicated the Islamist militant landscape in Pakistan. The emergence of the Pakistani Taliban – an amalgam of anti-state militants that formed in 2007 in reaction to the Pakistan military’s storming of the notorious Red Mosque in the heart of Islamabad – has threatened to destabilize the nation. The Pakistani Taliban has conducted countless terrorist attacks throughout the country over the last nine years, killing nearly 30,000 civilians and security forces, and prompting a major Pakistan Army operation against the militants during the last two years. 


Pakistan will continue to grapple with its status as a Muslim constitutional democracy, and with developing ways to channel Islamist ideologies that have played a significant role in its identity since 1947. While Islamist political parties are unlikely to take power in the near future, they will continue to influence the country’s legal framework and political discourse in ways that restrict personal freedoms, subordinate women and minorities, and enhance the role of clergy within the country’s democratic institutions. While societal attitudes will also shape Islamist trends in Pakistan, it can be argued that the military’s posture and attitude toward violent Islamists will be the single most important factor in determining the future direction of the country, i.e., whether it remains positively engaged with Western countries or takes a decisively Islamist turn that severs its traditionally strong relations with the United States.

Level of Islamist Activity: 
Islamist Activity: 

Pakistan’s Federally Administered Tribal Areas (FATA), which consist of seven semi-autonomous tribal agencies along the border with Afghanistan, constitute one of the most dangerous terrorist safe havens in the world today. In 2002, al-Qaeda’s leadership moved from Afghanistan into Pakistan’s North and South Waziristan sections of the tribal border areas, where they established networks with like-minded Pakistani groups such as the Jaish-e-Muhammed (JeM) and the Lashkar-e-Taiba (LeT).1 The Obama administration’s aggressive campaign of drone strikes in the region from 2010–2012 has helped degrade al-Qaeda’s leadership ranks and disrupted the group’s ability to plan and carry out international terrorist attacks. Pakistani denunciations of the drones for infringing on the country’s sovereignty and complaints from international human rights organizations about civilian casualties resulting from drone strikes, however, have led the U.S. administration to curb their use in recent years. All told, there have been over 400 U.S. drone strikes in Pakistan since January 2008, including the strike that killed Taliban leader Mullah Akhtar Mansour in Pakistan’s Baluchistan province in May 2016.2

Pakistan has long relied on violent Islamist groups to accomplish its strategic objectives in both Afghanistan and India. Pakistan’s support for groups that fight in Afghanistan—namely the Afghan Taliban and the Haqqani network—and those that primarily attack India (like the JeM and LeT) remains undiminished, even as it has stepped up its military operations in the tribal border areas against the Tehrik-i-Taliban Pakistan (TTP, or the Pakistani Taliban). 

There are around 150,000 Pakistani troops deployed along the Pakistan-Afghanistan border. Since 2002, the U.S. has provided nearly $14 billion to Pakistan in the form of Coalition Support Fund (CSF) reimbursements for Pakistan’s military deployments and operations along the Afghan border.3     

The Afghan Taliban

Pakistan’s military and intelligence services (particularly the Inter-Services Intelligence Directorate, or ISI) historically have had close ties with the Afghan Taliban, which ruled Afghanistan from 1996–2001. Before the terrorist attacks of September 11, 2001, the Pakistani government openly supported and recognized Taliban rule in Afghanistan. Although Pakistani officials largely disagreed with the Taliban’s harsh interpretation of Islam, they viewed the movement as their best chance to achieve their own strategic objectives in the region. Pakistan continued to support the Taliban into the late 1990s, long after Osama bin Laden took refuge there in 1996 and despite the growing problems that it created in Islamabad’s relations with Washington. Pakistan’s high-stakes policy vis-à-vis the Taliban derived from its aims of denying India, as well as Iran and the Central Asian countries, a strong foothold in Afghanistan and ensuring a friendly regime in Kabul that would refrain from making territorial claims on Pakistan’s Pashtun areas along the Pakistan-Afghanistan border.

Despite pledging to break ties with the Taliban after the U.S. invasion of Afghanistan in 2001, Islamabad failed to crack down forcefully on its leaders or to actively disrupt their activities in Pakistan. Indeed, U.S. officials have acknowledged that officials within Pakistan’s Inter-Services Intelligence (ISI) directorate maintain relationships with Afghan Taliban leaders and see benefits in keeping good ties with the Taliban in the expectation that the Taliban will again play a role in Afghan politics.4

Hopes for a negotiated Afghan settlement were raised in July of 2015, when Pakistan played host to face-to-face talks between the Afghan government and Taliban leaders. However, weeks later, just before a second round of talks was scheduled to be held, reports surfaced that Taliban supreme leader Mullah Omar had died two years prior, causing disarray within the Taliban movement. Pakistan helped install Omar’s successor, Mullah Akhtar Mansour, who was subsequently killed in a U.S. drone strike on May 21, 2016. The leadership crisis within the Taliban and escalating Taliban violence in Afghanistan, including a major truck bombing in Kabul on April 19th that killed nearly 65, have closed the door on negotiations for the foreseeable future.       


The unilateral U.S. raid in Abbottabad, Pakistan on May 2, 2011, that eliminated Osama bin Laden exposed deep fissures in U.S.-Pakistan relations. Pakistanis were incensed that the U.S. did not take its leadership into confidence before the raid. U.S. officials, on the other hand, were incredulous that the world’s most wanted terrorist could live in a Pakistani garrison town for six years without the knowledge of officials within the military establishment. U.S. Senator Susan Collins (R-Maine) said the bin Laden killing revealed the “double-game” Pakistan is playing and called for stricter conditions on U.S. aid to the country.5 U.S. Secretary of State Hillary Clinton told Members of Congress in June 2011 that a review of intelligence turned up no information indicating that top Pakistani leaders knew about bin Laden’s presence in Abbottabad. She added, however, that it was possible that lower-level Pakistani officials were involved in protecting the international terrorist. 

Pakistan’s subsequent arrest of a Pakistani doctor, Shakil Afridi, who helped the U.S. track bin Laden’s whereabouts through a fake vaccination campaign, was a further blow to bilateral relations. Afridi was initially sentenced to 33 years in prison by a Pakistani tribal court on trumped-up charges of supporting a militant group. In August 2013, however, the sentence was overturned, and a retrial was ordered.6 Pakistani authorities privately acknowledge he is being punished for helping the CIA. 

The Obama administration’s intensive drone campaign in Pakistan’s tribal border areas has helped degrade al-Qaeda and hindered its ability to plot and train for terrorist attacks across the globe. Pakistani officials and media outlets regularly criticize the drone missile strikes as a violation of Pakistani sovereignty, but the program appears to be at least tacitly accepted at the highest levels of the Pakistan government. Of more than 400 drone strikes in Pakistan since 2004, only the strike on Mansour in May and one other have taken place outside the tribal areas. The U.S. attack on Mansour angered Pakistani officials, who called it a “violation of sovereignty.” 

Due to Pakistani public anger over the drone campaign and complaints from human rights organizations about the number of civilian casualties, the U.S. administration has reduced considerably its reliance on drones. There were only 10 drone strikes in Pakistan in 2015, down from a peak of 128 strikes in 2010.

Tehreek-e-Taliban Pakistan (TTP)

The Tehreek-e-Taliban Pakistan (TTP), an amalgamation of Pakistani militant groups loosely affiliated with al-Qaeda and the Afghan Taliban, was formed in 2007 and has conducted numerous suicide attacks that since 2012 have killed over 9,000 Pakistani civilians and 2,400 Pakistani security forces.7

In the six weeks before Pakistani elections in May 2013, the TTP took responsibility for attacks that killed scores of election workers and candidates, mainly from the secular-leaning political parties. Nawaz Sharif’s Pakistan Muslim League/Nawaz (PML/N) party ran on a campaign of supporting negotiations with the TTP and failed to denounce the attacks on the electoral process.  Six months after winning the elections, the Nawaz Sharif government offered to engage in talks with the TTP. The TTP-government talks officially started in January 2014 but did not last long. The TTP claims of instituting a cease-fire were undermined by continued attacks against civilians and security forces. 

Talks broke down altogether following a major TTP attack on the Karachi airport that killed 36 in June 2014. One week later, the Pakistani military announced the launch of a new military offensive against TTP bases in North Waziristan called Zarb-e-Azb (“Strike of the Prophet’s Sword”). The Pakistani Army intensified their counterterrorism operations following an attack on a military school in Peshawar in December 2014 that killed 130, mostly children. Military operations in the FATA reportedly contributed to a nearly fifty percent decline in the number of terrorist attacks in the country in 2015, as compared to 2014. 

The National Action Plan (NAP) to combat terrorism passed by the Pakistani parliament in January 2015 has further contributed to the decrease in terrorist attacks, as well as laid initial groundwork for delegitimizing extremist ideologies. The plan includes steps like lifting the moratorium on the death penalty for terrorists, establishing special military courts to try terrorists, curbing the spread of extremist literature and propaganda on social media, freezing the assets of terrorist organizations, and forming special committees, comprised of army and political leaders, in the provinces to implement the NAP.

Still, Pakistan has a long way to go in reversing the tide of extremism and terrorism in the country, as evidenced by two major terrorist attacks that occurred earlier this year. On January 20, militants stormed a university in the Pakistani city of Charsadda, killing at least 20 students and teachers. Afghanistan-based TTP leader Omar Mansour claimed credit for the attack (Mansour’s faction of the TTP was also behind the 2014 attack on the school in Peshawar).9 A U.S. drone strike in eastern Afghanistan subsequently killed Mansour in July of 2016. 

Another splinter group of the TTP, Jamaat-ul-Ahrar, was responsible for a suicide bombing at a park in Lahore this past Easter. The group said it directly targeted Christians and that the bombing was a message to the Pakistani government that “we will carry out such attacks until Sharia is imposed in the country.”10 While the attack was directed at Christians, most victims were Muslim, and about half of the 72 killed were children.   

The Haqqani Network

Jalaluddin Haqqani—a powerful independent Afghan militant leader whose followers operate in the border areas between Khost in Afghanistan and North Waziristan in FATA—reportedly died in 2014. Haqqani had been allied with the Afghan Taliban for nearly 20 years, having served as tribal affairs minister in the Taliban regime in the late 1990s, and was known to be close to Pakistan’s intelligence service. Jalaluddin’s son, Sirajuddin, has taken over operational control of the militant network and currently serves as the number two leader of the Afghan Taliban.   

The Haqqani network has been a major facilitator of the Taliban insurgency in Afghanistan, and responsible for some of the fiercest attacks against U.S. and coalition forces. Haqqani forces were responsible for a suicide attack against the Indian embassy in Kabul in July 2008 that killed two senior Indian officials and over 50 others; a suicide attack on a CIA base in Khost Province in December 2009 that marked the most deadly attack on the CIA in 25 years; a multi-hour siege of the U.S. embassy in Kabul in September 2011; and—most recently—a major truck bombing in Kabul on April 19, 2016 that killed 65.

The source of the Haqqanis’ power lies primarily in their ability to forge relations with a variety of different terrorist groups (al-Qaeda, the Afghan Taliban, the Pakistani Taliban, and India-focused groups like the Jaish-e-Muhammed), while also maintaining links to Pakistani intelligence. Pakistani military strategists view the Haqqani network as their most effective tool for blunting Indian influence in Afghanistan. Credible U.S. media reports indicate that the Haqqani network, in cooperation with Pakistani intelligence, was responsible for the bombing of the Indian embassy in Kabul in July 2008, killing more than 50 people, including two senior Indian officials.11 U.S. officials have appealed to Pakistani leaders to crack down on the Haqqani network, but have been rebuffed with declarations that the Pakistani military is over-stretched and incapable of taking on too many militant groups at once. 

On September 7, 2012, under pressure from the U.S. Congress, the U.S. State Department listed the Haqqani Network as a Foreign Terrorist Organization (FTO). An organization designated an FTO is subject to financial and immigration sanctions. The designation also publicly stigmatizes the organization, which can help garner cooperation from foreign governments. The U.S. has killed several Haqqani network leaders in Afghanistan and in Pakistan’s tribal border areas since the FTO designation. 

The U.S. has also begun to block military aid to Pakistan due to its failure to crack down on the Haqqanis. The U.S. withheld $300 million in CSF payments to Pakistan in FY 2015 because the administration could not certify to Congress that Pakistan’s military offensive in the tribal border areas included operations against Haqqani bases.12 Furthermore, Congress blocked U.S. funding for the transfer of eight F-16 aircraft to Pakistan in the first half of 2016 because of Islamabad’s lack of action against the Haqqani sanctuary within its borders.13     

Lashkar-e-Taiba and Jaish-e-Mohammed

Groups like the Lashkar-e-Taiba (LeT) and Jaish-e-Mohammed (JeM, formerly the Harakat-ul-Ansar) focused their attacks throughout the 1990s on Indian security forces in Jammu and Kashmir, but now conduct attacks throughout India and target both Indian and Western civilians. The Pakistani government’s failure to shut down groups like JeM and LeT, who were responsible for the November 2008 attacks in Mumbai, is creating instability in the region and increasing the likelihood of additional international attacks, particularly against India, but also involving citizens of other nations. In March 2010, Pakistani-American David Headley, who was arrested in Chicago in early October 2009, pleaded guilty in a U.S. court to involvement in both the Mumbai attacks and a plot to attack the offices of a Danish newspaper for publishing caricatures of the Prophet Mohammed. In four days of testimony and cross-examination, Headley detailed meetings he had with a Pakistani intelligence officer, a former Army major, and a Navy frogman, all of whom were among the key players orchestrating the assaults. Headley’s revelations have raised questions about whether there was official Pakistani involvement in the Mumbai attacks.14 

Following the Mumbai attacks, Islamabad responded to U.S. and Indian pressure by arresting seven LeT operatives, including those that India had fingered as the ringleaders of the attacks: Zaki ur Rehman Lakhvi and Zarar Shah. The Pakistani government also reportedly shut down some LeT offices throughout the country. Despite these actions, there are indications that the LeT continues to operate relatively freely in the country. Pakistan released from detention LeT founder Hafez Muhammed Sayeed in June 2009, when the Lahore High Court determined there was insufficient evidence to continue his detainment. Sayeed has taken an increasingly public role in Pakistan and frequently speaks at political rallies, where he calls for jihad against India. In 2012, the U.S. issued a $10 million reward for information leading to his arrest and conviction.15 As further evidence of its unwillingness to act against the LeT, Pakistan released Zaki ur Rehman Lakhvi from jail in April 2015, just days after the U.S. approved the sale of nearly $1 billion in military equipment to Pakistan.

The LeT has put down roots in Pakistani society, especially in central and southern Punjab, through its social welfare wing, the Jamaat-ud-Dawa (JuD), which runs schools and medical clinics. The headquarters of the LeT/JuD is a 200-acre site outside Lahore in the town of Muridke. The JuD increased its popularity through its rapid response in helping victims of the October 2005 earthquake in Pakistani Kashmir. The U.S. government views the JuD as a surrogate or front organization of the LeT. The U.S. State Department designated the LeT as a Foreign Terrorist Organization in December 2001, and later included the JuD on the Specially Designated Global Terrorist Designation list as an alias of the LeT.16 On December 11, 2008, the United Nations Security Council imposed sanctions on JuD, declaring it a global terrorist group.17

There are well-known links between both the LeT and JeM to international terrorism. Shoe bomber Richard Reid apparently trained at a LeT camp in Pakistan; one of the London subway bombers spent time at the LeT complex in Muridke; and al-Qaeda leader Abu Zubaydah was captured from an LeT safe house in Faisalabad, Pakistan. The LeT signed Osama bin Laden’s 1998 fatwa calling for Muslims to kill Americans and Israelis. 

Reports indicate that one of the prime suspects in the 2006 London airliner bomb plot had family ties to Maulana Masood Azhar, the leader of JeM. The JeM has also been linked to the kidnapping and brutal murder of Wall Street Journal reporter Daniel Pearl in January 2002. Pakistan officially banned the JeM in 2002, but Azhar has never been formally charged with a crime. Indeed, reports indicate Masood Azhar addressed a large public rally in Pakistan via phone in early 2014 and called on his supporters to resume jihad against India. Furthermore, the JeM conducted a major attack on the Indian air base at Pathankot in early January of 2016, just six days after Indian Prime Minister Narendra Modi had made a surprise goodwill visit to Lahore, where he met with Pakistani Prime Minister Nawaz Sharif.

The Islamic State (ISIS)

ISIS has sought to gain the allegiance of various terrorist groups in the region and in January 2015 officially announced the formation of its Khorasan “province.” Khorasan is an Islamic historical term used to describe the area encompassed by Afghanistan, parts of Pakistan, and parts of other countries bordering Afghanistan. According to the relevant Hadith (sayings attributed to the Prophet Muhammad), South-Central Asia plays a key role in establishing a global caliphate. The Hadithcontains references to the Ghazwa-e-Hind (Battle of India), where the final battle between Muslims and non-Muslims before the end times will supposedly take place. One Hadith further says that an army with black flags will emerge from Khorasan to help the Mahdi (the prophesied redeemer of Islam) establish his caliphate at Mecca.18  

So far, only a handful of TTP leaders and a few disgruntled Afghan Taliban leaders have pledged their allegiance to ISIS leader Abu Bakr al-Baghdadi. The Pakistan-based anti-Shi’a sectarian outfit Jundullah reportedly pledged support to ISIS in late 2014.19 The number of fighters that have traveled from South Asia to fight with ISIS in Iraq and Syria also is relatively low. The International Centre for the Study of Radicalization estimates that around 500 fighters have travelled from Pakistan to join the ranks of the group.20  In July 2015, a U.S. drone strike in the eastern Afghan province of Nangahar killed more than two dozen ISIS fighters, including Shahidullah Shahid, former spokesman for the Pakistani Taliban, who had defected to ISIS ranks the year before.21

ISIS’ inability so far to make significant inroads into Pakistan is largely due to the well-established roots of al-Qaeda in the region. There is some concern that ISIS may eventually gain influence among the educated urban middle class in Pakistan since it has had success in recruiting among this cohort globally. However, most analysts are largely skeptical about the future prospects of ISIS in Pakistan.22

Al-Qaeda leader Ayman al-Zawahiri has sought to strengthen relations with Pakistan-based terrorist groups and make inroads with the Muslim populations in other parts of South Asia to help fend off ISIS encroachment. In September 2014, Zawahiri made a video announcement launching an al-Qaeda wing in the Indian Subcontinent (AQIS). In the video, Zawahiri assures Muslims in India, Bangladesh, and Burma that the organization “did not forget you and that they are doing what they can to rescue you from injustice, oppression, persecution, and suffering.”23 Just two days after the launch of AQIS, the group attempted to attack a Pakistani navy frigate in order to use it to target American naval assets in the Indian Ocean.

Islamism and Society: 

The strategic environment in South Asia over the last 30 years, and the Pakistani response to regional challenges, has influenced Islamist trends in society and heightened religious-inspired violence. The war against the Soviets in Afghanistan in the 1980s and the Islamization policies of Pakistani president General Zia ul-Haq during the same period strengthened Islamist political forces and puritanical sects like the Deobandis over the more moderate Barelvis.24 The influence of Sufism, dating back to the eighth and ninth century in South Asia, also has had a moderating influence on how most Pakistanis practice and interpret the Islamic faith. 

Muslim revivalist movements developed late in the nineteenth century in South Asia in response to the decline in Muslim power in the region and as a reaction to British colonial rule. The first attempt to mobilize pan-Islamic sentiment on the Subcontinent was in 1919 through the launching of the Khilafat movement, which agitated against the abolition of the Ottoman caliphate.25 Although the movement dissolved after the Turkish government abrogated the Muslim caliphate in 1924, it roused Muslim political consciousness and catalyzed a sense of communal identity.26 

The Jamaat-e-Islami was founded by Islamic scholar Maulana Abul Ala Maududi in 1941. Maududi came of age as British colonial rule was ending on the Subcontinent and an Indian national identity was developing. Witness to Hindu-Muslim communal tensions, Maududi believed the only way Muslims could safeguard their political interests was to return to a pure and unadulterated Islam that would not accommodate Hindus. He denounced nationalism and secular politics and held that the Islamic state was a panacea for all the problems facing Muslims. He further held that for Muslims to mobilize their resources against the Hindus, they had to break free of any Western influences.27 Reflecting Maududi’s early linking of the Muslim struggle with both Indian Hindus and western forces, modern Islamist extremist literature in Pakistan draws parallels between British colonial rule in the nineteenth century and U.S. ascendancy since the middle of the twentieth.28 

In contrast with Maududi, Pakistan’s founding father and leader of the Muslim League, Muhammed Ali Jinnah, supported the idea of Islam serving as a unifying force, but envisioned the country functioning largely as a secular and multiethnic democratic state. Thus, although the argument to establish a separate Pakistani state was based on religious exclusivity, Jinnah’s ultimate goal was not to establish Pakistan as a theocratic state.29 However, soon after the creation of Pakistan, debate about the role of religion in the country’s constitutional and legal systems was increasingly influenced by the idea that Islamic principles should inform the conduct of the state.30 

Maududi’s contrasting vision for Pakistan created problems for him and the JI during the early years after partition. Pakistani authorities questioned the allegiance of JI members to the state and even incarcerated Maududi for his controversial positions on the Indo-Pakistani dispute over Kashmir.31 After spending time in jail, Maududi eventually stopped questioning the legitimacy of the Pakistani state and focused on encouraging Islamization of the government and the adoption of an Islamic constitution. 

Today’s Jamaat-I-Islami (JI) political party in Pakistan, led by Siraj-ul-Haq, draws most of its support from middle class urban Pakistanis. It has generally performed only marginally at the polls, capturing about five percent of the vote in most elections held during the last two decades. The party’s influence on Pakistani politics and society outweighs its electoral performance, though, primarily because of its effectiveness in mobilizing street power, its ability to influence court cases, and its adeptness at using Pakistan’s Islamic identity to bring pressure on military and democratic governments alike to adopt aspects of its Islamist agenda.32 In the 2002 elections, the JI formed an alliance with five other religious political parties, and the coalition garnered over 11 percent of the national vote. The resulting coalition of Islamist parties grabbed enough votes in Khyber Pakhtunkhwa (KPK) to form the government, marking the first time the Islamists were charged with running a provincial government (see below). 

The other major Islamist movement in South Asia is the Deobandi movement. This movement originated in 1866 in the city of Deoband in the Indian state of Uttar Pradesh with the establishment of the Dur ul-Ulum madrassa (a Muslim religious school), which is still the largest operating Deobandi madrassa. Deobandism was a reformist movement that developed in reaction to British colonialism and from the belief among Muslim theologians that British influence on the Indian subcontinent was corrupting the religion of Islam. The Deobandis solidified a puritanical perspective toward Islam for South Asian Muslims, much as the Wahhabis have done in present-day Saudi Arabia.33 

Although Deobandi clerics were initially concerned with strengthening the Islamic character of individuals and society, several of them later became politically focused and joined the Jamiat Ulema-e-Hind (JUH), a political party established in pre-partition India in 1919.34 In the lead-up to partition, the Deobandis split between those who supported Gandhi’s Indian National Congress and those who supported the creation of a separate state of Pakistan as proposed by Muslim League leader Muhammed Ali Jinnah. The pro-Muslim League faction became the Jamiat Ulema-e-Islam (JUI), while the JUH maintained links with the Indian National Congress, arguing that the creation of Pakistan would divide and weaken the Muslims of the Subcontinent.35

The Deobandis gained considerable strength during the war against the Soviets in Afghanistan in the 1980s when madaris (plural of madrasa) mushroomed in Pakistan, partially to accommodate the three million Afghan refugees that fled there. The Taliban leaders who made their debut in Kandahar, Afghanistan in 1994 came mostly from these Deobandi madaris.36 As a political party, JUI draws support from rural voters, mostly among Pashtuns in the northwest.

Three wars and several military crises with India have also bolstered the influence of religious extremists, with the backing of the Pakistani state. During the 1990s, the JI focused its agenda on supporting Kashmiri militants, while the JUI turned most of its attention to supporting the Taliban in Afghanistan. More recently, both the JUI and JI have rallied their political supporters against U.S. policies in the region, taking advantage of high levels of anti-American sentiment fueled by the post 9/11 American and NATO military presence in Afghanistan and U.S. pressure on Pakistan to tackle terrorists on its own soil. Most Pakistanis blame their country’s counterterrorism cooperation with the U.S.—not past support for religious extremists—for the incessant suicide bombings and attacks across the nation that have claimed more than 9,000 civilian lives since 2012. 

The erosion of respect for religious pluralism in Pakistan has also been facilitated by exclusionary laws and the proliferation of minority-hate material in public and private school curriculums. Several studies have also documented a broad-based connection between madrassa education and the propensity toward gender, religious, and sectarian intolerance and militant violence in Pakistan. Madaris (the plural of madrassas) are spread throughout Pakistan, but most analysts believe that only about 5–10 percent of Pakistani school children attend these Islamic seminaries. A number of these schools are financed and operated by Pakistani Islamist parties, such as the Jamaat-e-Ulema Islam (JUI), and by Pakistani expatriates and other foreign entities, including many in Saudi Arabia. In a seminal study entitled “Islamic Education in Pakistan,” South Asia scholar Christine Fair notes that while there is little evidence that madaris contribute substantially to direct recruitment of terrorists, they do help create conditions that are conducive to supporting militancy.38 While mainstreaming and expanding the curriculums of madaris is part of reversing extremist trends, it is equally important for Pakistan to improve and modernize its public education sector and to revise textbooks that encourage an intolerant and militant culture.

Discrimination against religious minorities—including Christians, Hindus, Sikhs, Ahmadis, and Shi’a—has led to a threefold increase in religious and sectarian violence in the country over the last 30 years. The rising violence against the Shi’ite community (which makes up about 25 percent of Pakistan’s total population) has been part of the upward trend in sectarian attacks. In May 2015, gunmen attacked a bus in Karachi, killing 45 Ismaili Shi’a. In January 2015, at least 61 people were killed after a bombing at a Shi’a mosque in Shikarpur, while two years prior in January and February 2013, sectarian attacks including bombings in Quetta killed nearly 200 Shi’a. 

In recent years, most of the attacks against Pakistani Shi’a have been carried out by the Lashkar-e-Jhangvi (LJ), a Sunni militant organization that receives inspiration and support from al-Qaeda. The Pakistan government has begun to crack down on LJ and target its leadership over the past year. In July 2015, one week after his arrest, LJ founder and supreme leader Malik Ishaq and over a dozen of his followers were killed in a police encounter.39

The minority Ahmadi community also is suffering severely from the growing culture of religious intolerance in Pakistan. The Ahmadiyya Jamaat has approximately 10 million followers in the world, including approximately 3 to 4 million in Pakistan. Toward the end of the 19th century, Mirza Ghulam Ahmad (1835-1908), founder of the Ahmadiyya Jamaat, broke with centuries-old Islamic dogma by claiming to be an Islamic prophet. (Mainstream Muslims believe that the Prophet Mohammad was the last prophet.) Six years after Pakistan’s independence, Islamists led by Anjuman-i-ahrar-i-Islam (Society of Free Muslims) started a mass movement to declare the Ahmadi sect as non-Muslim, arguing that Ahmadiyya was an entirely new religion that should not be associated with Islam. In late May of 2010, militants armed with hand grenades, suicide vests, and assault rifles attacked two Ahmadi mosques, killing nearly 100 worshippers.40 Human rights groups in Pakistan criticized local authorities for their weak response to the attacks and for their failure to condemn the growing number of kidnappings and murders of members of the Ahmadi community. In December 2014, a member of the Ahmadi community in Gujranwalla was shot and killed five days after an extremist cleric called Ahmadis “the enemy” in a rant on a popular Pakistani television show.

Christians also are increasingly bearing the brunt of rising Islamist extremism in Pakistan. There have been numerous incidents of violence against Christians and their worship areas in the last few years. In the largest attack to date targeting the Christian community, on September 22, 2013, 85 people were killed during Sunday services when dual suicide bombers attacked a church in Peshawar, Pakistan. The group responsible for the attack, a faction of the Tehrik-e-Taliban Pakistan (TTP), said they were retaliating against U.S. drone strikes in Pakistan’s tribal border areas. More recently, a splinter group of the TTP carried out a suicide attack against Christians celebrating the Easter holiday at a park in Lahore in March 2016.

The public reaction to the early 2011 murders of two senior Pakistani officials for advocating changes to the country’s blasphemy laws demonstrates growing religious intolerance within Pakistani society. When Pakistani Punjab Governor Salman Taseer was assassinated on Jan 4, 2011, after pushing for scrapping the blasphemy laws (which are often misused against religious minorities), several hundred Pakistani clerics signed a statement condoning the murder and warning Pakistanis against grieving his death. Two months later, Pakistani Minority Affairs Minister Shahbaz Bhatti was also gunned down. Bhatti’s murderers left pamphlets at the scene of the crime, explaining that they killed him because of his opposition to the blasphemy laws. 

The London-based think tank Quilliam warned in its August 2009 report that Pakistani youth are a prime target for Islamist recruitment.41 With the segment of Pakistan’s population between ages 15-24 estimated to be around 36 million, and those below the age of 15 an additional 58 million,42 the need for specific policies to counter the Islamist agenda is apparent. The Quilliam report argues that without the development of a compelling Pakistani identity, pan-Islamism is starting to fill the void.43 

There have been some recent signs that the Nawaz Sharif government is slowly seeking to reverse extremist trends in society. The most notable was the government’s follow-through with the execution of Mumtaz Qadri, the murderer of Salman Taseer. Despite street protests in all of Pakistan’s major cities against the execution of Qadri, the government resisted intervention against the Supreme Court’s decision, and the death sentence was carried out on February 29, 2016. 

The Supreme Court also agreed in 2015 to review the case of Asia Bibi. Bibi, a mother of five and a farmworker, was arrested in 2009 after her Muslim co-workers alleged that she had committed blasphemy during an argument about sharing a water bowl. In November 2010, she was sentenced to death by a Pakistani trial court—a decision that was upheld by the Lahore High Court in October 2014. The outcome of the review is still pending.    

The 2007 Red Mosque siege and the events that followed have played a significant role in Pakistani society’s current perception of Islamist movements. Early in 2007, students of the notorious Red Mosque in the heart of Islamabad, and an adjacent madrassa for women, launched a vigilante-like campaign to force their view of Islam on the Pakistani people. They burned CD and video shops, took over a local children’s library, and kidnapped women whom they accused of running a brothel, as well as several Pakistani policemen. 

On July 5, 2007, Pakistani troops started a clearing operation to force the students to vacate the mosque and madrassa. While 1,200 students surrendered and the government sought to negotiate a peaceful resolution, over one hundred armed militants hunkered down in the mosque and madrassa and vowed to fight until death. Five days later, military troops stormed the buildings. After two days of fierce fighting, the military gained control of the premises, but only after 19 soldiers and 62 militants were killed. 

The Pakistani public reacted negatively to the military operation, with Islamist circles questioning the use of force against the country’s own citizens and mosques, and more liberal commentators faulting the government for allowing the situation to get out of hand in the first place, noting the past strong ties of Pakistani intelligence to the mosque. The Islamist political parties faced a dilemma in that they largely agreed with the policies the Red Mosque leaders were pursuing but did not support the idea of engaging in violent confrontation with the government to achieve these goals.44 Following the military operation that ended the siege, then-JI leader Qazi Hussain held the state “wholly responsible” for the confrontation. In addition, the two Islamist parties hailed the Red Mosque militants as “mujahideen who fought for enforcing Islam in its true spirit.”45

However, ever since April 2009, when pro-Taliban militants moved from the Swat Valley into neighboring districts following a peace deal with the government, most observers have believed that the militants overplayed their hand and revealed their long-term intentions of expanding influence throughout Khyber Pakhtunkhwa (KPK). Pakistanis living outside of the northwest province had previously believed the Taliban’s activities could be contained within the tribal areas and Swat Valley. A video that circulated in the Pakistani national media in early April 2009 showing Taliban leaders whipping a young girl also helped turn Pakistani public opinion against the militants. 

In early 2009, the Pakistan military, with backing from the central government, pursued a peace deal with the pro-Taliban militant group, the Tehreek-e-Nafaz-e-Shariat-e-Mohammadi (TNSM, or “Movement for the Enforcement of Islamic Law”), whose objective is to enforce sharia throughout the country. In 2007, the movement succeeded in taking over much of the Swat Valley in the settled areas of KPK. The Pakistan military deployed some 12,000 troops to the area for 18 months in 2007-2008 before ceding the territory to the militants. The surrender of the valley occurred despite the overwhelming vote in favor of the secular Pashtun Awami National Party in the February 2008 elections, demonstrating that the people of the region did not support the extremists’ agenda but were merely acquiescing in the absence of support from the government to counter the militants. 

Tensions came to a head in mid-April 2009, when the pro-Taliban forces moved from the Swat Valley into the neighboring district of Buner. On April 24, 2009, under both Pakistani public and U.S. pressure, the Pakistan Army deployed paramilitary troops to the region and then-Chief of Army Staff (COAS) General Ashfaq Kayani sent a warning to the militants that the Army would not allow them to “impose their way of life on the civil society of Pakistan.”46 The statement was a positive first step in clarifying Pakistani policy toward the militants and was followed by aggressive military operations. By mid-summer, the Pakistan military cleared the militants from the Swat Valley, and normalcy began to return to the region.47

The Pakistani public was outraged when Malala Yousafzai—a fifteen year-old girl who openly advocated for the education of girls in the Swat Valley—was shot by militants in early October 2012 as she boarded a bus from school. Yousafzai miraculously survived the assassination attempt and continues to advocate for female empowerment and education. She is the youngest person ever to have won the Nobel Peace Prize.  

The Army’s resolve in fighting militants in the Swat Valley, and more recently in North Waziristan, signals greater clarity within the military establishment about the threat to the state from the Pakistani Taliban. However, there are few signs the Pakistani Army leadership is ready to accommodate U.S. requests to crack down on other groups that target U.S. and coalition forces in Afghanistan, like the Jalaluddin Haqqani network that operates out of North Waziristan and Afghan Taliban leaders that operate mainly from Quetta, Baluchistan.

Islamism and the State: 

Following the 9/11 attacks, former Pakistani President Pervez Musharraf broke off official ties with the Taliban, supported the U.S. invasion of Afghanistan, granted over-flight and landing rights for U.S. military and intelligence units, facilitated logistical supply to military forces in Afghanistan, and contributed substantially to breaking up the al-Qaeda network in the region. Pakistan helped captured scores of senior al-Qaeda leaders, most notably 9/11 mastermind Khalid Sheikh Mohammed. 

However, the government’s various relationships with Islamist groups were not entirely severed, and progress in this regard has been mixed. In addition to sporadic military operations, the Pakistani government in the past pursued several peace deals with the militants, which contributed to destabilizing the Pakistani state and facilitating insurgent attacks against coalition forces in Afghanistan. 

The first peace deal in March 2004, referred to as the Shakai Agreement, was interpreted by locals as a military surrender.48 A February 2005 peace agreement with now-deceased TTP leader Baitullah Mehsud also backfired, emboldening Mehsud to form the Tehrik-e-Taliban Pakistan. Baitullah Mehsud directed a string of suicide attacks against both Pakistani security forces and civilians in 2008-2009. Mehsud was killed by a U.S. drone strike in August 2009 and was replaced by Hakimullah Mehsud, who was also killed by a drone strike in November 2013. 

The Pakistan military remains powerful, despite the first successful peaceful transfer of power from one democratically-elected government to another in May 2013. Thus the country’s success in countering violent Islamist movements will largely be determined by both the military’s capabilities in beating back Islamist insurgencies in the northwest part of the country, as well as its policies toward violent extremist groups it continues to nurture. 

Throughout Pakistan’s troubled political history, both military leaders and democratic politicians have contributed to the Islamization of society and political discourse. Pakistan has endured military rule for about half its existence (during the periods 1958–1971, 1979–1988, and 1999–2008). Even when democratic governments have been in power, the Pakistani Army continued to wield tremendous influence, particularly on matters related to foreign policy and the country’s nuclear program. The Army leadership has proved itself adept at using religion and Islamist political parties to stifle political opposition. During the 2002 elections, then-President Musharraf pursued steps, such as campaign restrictions and candidate selection policies, which favored the Islamist parties over the democratic opposition, thus helping religious parties garner their greatest percentage of votes ever and catapulting the Islamist coalition to power in KPK. 

In contrast to their showing in the 2002 elections, Pakistan’s Islamist political parties performed poorly in the country’s February 2008 and May 2013 elections. In 2008, the JI boycotted the election, and the other Islamist parties garnered only two percent of the national vote. In 2013, the JUI/F won 10 seats, and the JI only three seats in the National Assembly. 

The democratic parties, during their tenures, have also sought to co-opt the religious parties in various ways and use religion to consolidate their power base. Pakistan’s first elected Prime Minister, Zulfiqar Ali Butto, passed a resolution in 1974 declaring Ahmadis to be non-Muslims. The legislation barred Ahmadis from calling themselves Muslims, calling their places of worship mosques, performing the Muslim call to prayer, and using the traditional Islamic greeting in public. In 1998, when he was serving his second stint as Prime Minister, Nawaz Sharif proposed a law to introduce sharia as the law of the land. If passed, it would have nullified the existing civil code and made Sharif the Amir-ul-Momineen (Commander of the Faithful) with absolute power. Fortunately, the motion failed.

What has been most damaging to the democratic character of Pakistan—and contributed significantly to the country’s current instability—has been the Pakistan military’s reliance on religious militants to achieve strategic objectives vis-à-vis Afghanistan and India.49 The Pakistani Army’s support for militancy as an instrument of foreign policy has eroded religious tolerance and created strong links between the Islamist political parties and militant groups.50 

The Obama administration has challenged the Pakistanis on their lack of consistency in countering terrorist groups in the region and their failure to crack down on the Afghan Taliban and related groups that threaten the U.S. and coalition mission in Afghanistan. The Kerry-Lugar bill passed by the Senate in September 2009 (the Enhanced Partnership with Pakistan Act of 2009) authorized $7.5 billion in civilian aid to Pakistan over a five-year period but also conditioned military assistance on Pakistani measures to address terrorist threats. Former U.S. Director of National Intelligence Admiral Dennis Blair testified before Congress on February 2, 2010, “Pakistan’s conviction that militant groups are strategically useful to counter India are hampering the fight against terrorism and helping al-Qaeda sustain its safe haven.”51

In September 2012, the Obama administration did not certify Pakistan for military aid because it failed to meet the counterterrorism benchmarks stipulated by the law. Instead the Administration took advantage of a national security waiver contained in the law to waive the conditions and thus allow U.S. military aid to continue to flow to Pakistan. In February 2013, the Administration again issued a waiver to allow the transfer of major defense equipment.  

More recently, the U.S. Congress has used its authority to block U.S. military aid for Pakistan. The National Defense Authorization Act (NDAA) for FY2015 stipulated that $300 million of the $1 billion in CSF funding appropriated for Pakistan could no longer be subject to Presidential waiver authority. Thus, when the Administration failed to certify that the Pakistan military’s operations in the tribal areas included attacking Haqqani Network bases, Congress blocked the transfer of $300 million in CSF payments to Pakistan. The NDAA for FY2016 authorized another $900 million in CSF funding for Pakistan, with $350 million being ineligible for waiver.  

The military confrontation following the siege of the Red Mosque in 2007, the aggressive military operations in the Swat Valley in 2009, and the on-going Zarb-e-Azb operations in North Waziristan against the TTP, all demonstrate that in certain situations the Pakistan military is prepared to confront extremists, even those with whom it previously had an intelligence relationship. The army links to religious militants revolve more around regional strategic calculations than deep sympathies with the Islamists’ ideology. Thus, while it may take time to fully sever ties between elements of the military/ISI establishment and Islamist militant groups, this outcome is certainly possible. Indications that the Red Mosque confrontation caused some dissent within the Army ranks demonstrate the challenges of convincing the Pakistan military to confront its former proxies without causing major discord within the only Pakistani institution capable of taking on the militants. Any such process will take time and circumspection in order to anticipate and minimize the chances of revolt inside the military ranks. 

The strength and professionalism of the Pakistani Army, combined with the democratic impulse of middle class Pakistanis who are familiar with a tradition of practicing moderate Islam, should act as bulwarks against a potential Islamist revolution similar to the one in Iran in 1979. However, until Pakistan takes a more comprehensive approach to defeating Islamist extremism within its borders by cracking down on all Islamist extremists (not just on those groups that attack the Pakistani state), Pakistan’s future will be at risk.  

The hardening stance toward Pakistan among Members of the U.S. Congress signals that America’s patience with Pakistan’s dual policies toward terrorism is wearing thin. While completely isolating Pakistan and disengaging with its leadership is not a realistic policy option, it is likely that U.S.-Pakistan relations will continue on a downward trend, unless there is a substantial change in Pakistan’s policies toward terrorist groups that threaten both regional stability as well as fundamental U.S. national security interests.


[1] Haider A.H. Mullick, “Pakistan’s Security Paradox: Countering and Fomenting Insurgencies,” Joint Special Operations University Report 09-9 (Hurlburt Field: JSOU Press, 2009), 50.
[2] Bill Roggio, “Charting the Data for U.S. Airstrikes in Pakistan 2004–2015,” Long War Journal, n.d.,
[3] K. Alan Kronstadt, “Direct Overt U.S. Aid Appropriations for and Military Reimbursements to Pakistan, FY2002-FY2017, Congressional Research Services Memo for Congress, February 24, 2016,
[4] “Senate Armed Services Committee Holds Hearing on the Situation in Afghanistan,” Congressional Testimony, General John R. Allen, Senate Armed Services Committee, March 22, 2012,
[5] Stephanie Condon. "After Osama Bin Laden's Death, Congress Puts Pakistan on the Hot Seat." CBSNews, 3 May 2011.
[6] "Bin Laden Doctor Shakil Afridi to Be Retried." BBC News, 29 Aug. 2013.
[7] “Fatalities in Terrorist Violence in Pakistan 2003-2016,” South Asia Terrorism Portal, n.d.,
[8] Pakistan Security Report 2015, Pak Institute of Peace Studies, n.d.,
[9] “Taliban faction releases video of four BKU attack militants,”, January 23, 2016, 
[10] Shaiq Hussain and Erin Cunningham, “Taliban Splinter Group Claims Attack on Christians at Pakistan Park; 60 dead,” Washington Post, March 27, 2016, at
[11] Mark Manzetti and Eric Schmitt, “Pakistanis Aided Attack in Kabul, U.S. Officials Say,” New York Times, August 1, 2008,
[12] Jamie Crawford. "US Holds up $300 Million for Pakistan over Terrorism." CNN, 4 Aug. 2016.
[13] Franz-Stefan Grady. "US Won't Subsidize Pakistan's Purchase of F-16 Fighter Jets." The Diplomat, 4 May 2016.
[14] Katherine Wojtecki, “Chicago Man Pleads Guilty to Terror Plots,”, March 18, 2010,
[15] "Rewards for Justice - Lashkar-e-Tayyiba Leaders Reward Offers." U.S. Department of State. 03 Apr. 2012.
[16] U.S. Department of State, Office of the Coordinator for Counterterrorism, Country Reports on Terrorism 2008 (Washington, DC: U.S. Department of State, April 30, 2009),
[17] Zahid Hussain and Eric Bellman, “Pakistan Says It May Outlaw Islamic Group,” Wall Street Journal, December 11, 2008,
[18] Husain Haqqani, “Prophecy and the Jihad in the Indian Subcontinent,” Current Trends in Islamist Ideology 18 (2015), 6.
[19] Farhan Zahid and Muhammad Ismail Khan, “Prospects for the Islamic State in Pakistan,” Current Trends in Islamist Ideology 20 (2016), 69.
[20] Peter R. Neumann, “Foreign fighter total in Syria/Iraq now exceeds 20,000; surpasses Afghanistan conflict in the 1980s,” International Centre for the Study of Radicalization, January 26, 2015,
[21] Sudarsan Raghavan and Tim Craig, “Suspected U.S. drone strikes kill key Islamic State figures in Afghanistan,” Washington Post, July 9, 2015,
[22] Zahid and Khan, “Prospects for the Islamic State in Pakistan.”
[23] Lisa Curtis, “Al-Qaeda Announces New Affiliate in South Asia,” The Daily Signal, September 4, 2015,
[24] For a discussion of the Barelvi school of Islamic thought, see Haider A.H. Mullick and Lisa Curtis, “Reviving Pakistan’s Pluralist Traditions to Fight Extremism,” Heritage Foundation Backgrounder no. 2268, May 4, 2009,
[25] Joshua T. White, Pakistan’s Islamist Frontier: Islamic Politics and U.S. Policy in Pakistan’s North-West Frontier Province (Arlington, VA: Center on Faith and International Affairs, 2008), 25.
[26] Seyyed Vali Reza Nasr, The Vanguard of the Islamic Revolution: The Jamaat-I-Islami of Pakistan (Berkeley, CA: University of California Press, 1994), 11.
[27] Ibid, 4-8.
[28] Husain Haqqani, “The Ideologies of South Asian Jihadi Groups,” Current Trends in Islamist Ideology 1 (2005), 12.
[29] Stephen Philip Cohen, The Idea of Pakistan, (Washington, DC: The Brookings Institution, 2004), 161.
[30] Fatima Mullick and Mehrunnisa Yusuf, Pakistan: Identity, Ideology, and Beyond (London: Quilliam, August 2009), 11.
[31] Nasr, The Vanguard of the Islamic Revolution, 121.
[32] White, Pakistan’s Islamist Frontier, 38.
[33] Mullick and Curtis, “Reviving Pakistan’s Pluralist Traditions to Fight Extremism.”
[34] White, Pakistan’s Islamist Frontier, 25.
[35] Ibid., 26.
[36] Haqqani, “The Ideologies of South Asian Jihadi Groups,” 21.
[37] Mullick and Curtis, “Reviving Pakistan’s Pluralist Traditions to Fight Extremism.”
[38] C. Christine Fair, “Islamic Education In Pakistan,” United States Institute of Peace, March 26, 2006,
[39] “Malik Ishaq: Pakistan Sunni Militant Chief Killed by Police,” BBC, July 29, 2015,
[40] Rizwan Mohammed and Karin Brulliard, “Militants Attack Two Ahmadi Mosques In Pakistan; 80 Killed,” Washington Post, May 29, 2010,
[41] Mullick and Yusuf, Pakistan: Identity, Ideology, and Beyond, 9.
[42] Ibid., 2.
[43] Ibidem, 9.
[44] Joshua T. White, “Vigilante Islamism in Pakistan,” Current Trends in Islamist Ideology 7 (2008), 56.
[45] Ibid, 59.
[46]“Pakistani Taliban Withdraw from Key Northwestern District,” Voice of America, April 24, 2009.
[47] Lisa Curtis, Testimony before the U.S. Senate Committee on Homeland Security and Governmental Affairs, Subcommittee on Federal Financial Management, Government Information, Federal Services, and International Security, July 7, 2009.
[48] C. Christine Fair and Seth G. Jones, “Pakistan’s War Within,” Survival 51, no. 6 (December 2009–January 2010), 171.
[49] Yusuf, “Prospects of Youth Radicalization in Pakistan: Implications for U.S. Policy,” 10; Frederic Grare, Reforming the Intelligence Agencies in Pakistan’s Transitional Democracy (Washington, DC: Carnegie Endowment for International Peace, 2009), 23.
[50] Yusuf, “Prospects of Youth Radicalization in Pakistan: Implications for U.S. Policy,” 19-20.
[51] Dennis C. Blair, “Annual Threat Assessment of the US Intelligence Community for the Senate Select Committee on Intelligence,” February 2, 2010,