Pakistan is facing a major political and security crisis, putting large numbers of members of minorities in grave danger. In 2009, the country's security situation deteriorated, with repeated targeted attacks by militant groups killing scores of people. In the early part of the year, Tehreek-e-Nifaz-e-Shariat-e-Mohammadi, an organization affiliated with the Taliban, agreed to a ceasefire after the government gave the go-ahead for the imposition of Sharia (Islamic law) in the NWFP's Swat Valley. The ceasefire did not last and, in May 2009, the government launched a major military offensive against Taliban positions in Swat. The fighting also spread to Buner, Shangla and Dir districts. Over 2 million people, mostly ethnic Pashtuns, fled the area. Religious minority Sikhs and Christians were also displaced but tended to travel beyond the temporary camps set up in the NWFP, MRG reported in its August 2009 briefing paper, Pakistan: Minorities at Risk in the North-West. There were reports that Pashtun displaced in other provinces were being discriminated against, through excessive demands for security documents based on a presumption that they were Taliban supporters. This was despite the fact that many local Pashtun communities had put up fierce resistance to the insurgents. By July 2009, the fighting had ceased and people were allowed to return home, but MRG warned that security guarantees were limited, particularly for minorities. Moreover, underlying frustrations remained among Pashtun communities in the NWFP over lack of investment and land reform, issues that the Taliban has exploited.

In October 2009, the Pakistani government renewed its military offensive against Taliban strongholds, this time in South Waziristan, a Federally Administered Tribal Area (FATA) west and south-west of the NWFP provincial capital, Peshawar. South Waziristan is home to ethnic Pashtuns divided into tribes such as Waziris, Burkis and Mahsuds. Over 300,000 people were displaced as a result of the fighting, UN agencies reported. In December, the government declared the campaign over, saying that much of the Taliban's military infrastructure had been destroyed. A day later, media reports stated that the prime minister retracted his comments and said that the campaign was ongoing and may extend into North Waziristan. At the end of 2009, the UN High Commission for Refugees (UNHCR) reported that 280,000 people from South Waziristan remained displaced.

The Pakistani province of Balochistan, which is home to the Baloch minority as well as to Pashtuns, is currently one of the most explosive parts of the country. In February 2009, the head of UNHCR's office in the provincial capital Quetta, John Solecki, was kidnapped by the Balochistan Liberation United Front. Solecki's driver Syed Hashim was killed in the incident. According to media reports, the separatist group made three demands to the Pakistani government, including the release of 141 women arrested by the Pakistani government and the investigation of more than 6,000 alleged missing persons. In April, Solecki was released, and in a subsequent incident three Balochi elders were killed. The government claimed they were killed accidentally in a shoot-out, but the armed group insists that the government conducted the killings. People have been extra-judicially killed, arbitrarily arrested, detained, made to disappear and tortured by security forces in Balochistan, according to Asian and international human rights groups. The area has long been marginalized and, due to increasing poverty, Balochis are becoming dissatisfied and feel disenfranchised by the government. Moreover, given that Balochistan, and Quetta in particular, is an important base for the Taliban, there is a clear risk that civilians will be drawn into the conflict between it and the government.

Inter-ethnic violence broke out in Karachi in February 2009 between Mohajirs and Pashtuns, during which at least 24 people were killed. Mohajirs are descendants of Muslim refugees from India, who came to Pakistan after independence and partition in 1947. Though the attacks had an ethnic dimension, they were driven by political factors and linked to political parties. Armed paramilitary troops were sent out to patrol the streets and ensure security, preventing further clashes.

Pakistan's religious minorities continued to face a series of human rights violations and targeted attacks. The country's Christian population face increasing threats to their lives from the Pakistani Taliban, as well as other Muslim extremists, who demand that they convert to Islam. At village level, Christians are also vulnerable to arbitrary arrest and detention, as they have limited access to justice. In one incident, a church in Bannu, NWFP, was vandalized on 11 May 2009. The intruders burned Bibles as well as the altar, and smashed windows and fans. Christians were among those who were displaced by the fighting in Swat, although they mostly chose to go into the provincial capital Peshawar, rather than to the camps.

The violence faced by Christians was not limited to Pakistan's north-west. In August 2009, eight Christians were burnt alive by Muslim extremist groups in Gojra in Punjab province, during violent attacks over rumours that a Qur'an had been desecrated. In a subsequent report, the independent Human Rights Commission of Pakistan stated that the attacks were premeditated and that local officials had been aware of the threat. Following the attack, Prime Minister Yousuf Raza Gilani announced plans to review 'laws detrimental to religious harmony'. However, Pakistan's infamous blasphemy law (clauses 295-B and 295-C of the Penal Code) remains in place and is used as a basis for arresting and detaining members of religious minorities.

A church was burnt down in Punjab's Sialkot district in September 2009, again following rumours that a Qur'an had been desecrated. Also in September, a Christian man was found dead in a jail cell. The Pakistan Christian Congress called on judicial authorities to conduct a full and impartial investigation into the killing. Police said it was suicide, but local Christian clergy said they found torture marks on his body.

Sections of the Sikh community in Pakistan were harassed and faced economic difficulty over 'jizya', a religious tax imposed by the Taliban in areas controlled by them. The targeting of Sikhs was particularly acute in the Orakzai FATA, MRG's own research found. Taliban demanded jizya from 40 Sikh families living there; they also seized a member of the Sikh community and demanded a ransom. He was released after the Sikh community paid half the amount, before fleeing the area. In the process, the Taliban destroyed 11 Sikh homes.

Pakistan's Shia minority was also targeted during the course of 2009. In February, an explosion at a procession to mark the death of Shia religious leader Imam Hussain in Dera Ismail Khan, NWFP, killed 15 people and injured dozens. Later in the month, at least 25 people were killed and over 150 injured, also in Dera Ismail Khan, at the funeral of a local Shia leader who had been killed by militants the day before. In April, in Chakwal, 22 people were killed and 30 injured in another suicide bombing targeting a Shia religious gathering.

Incidents of forced conversion continued to be reported in Pakistan, often linked to gender-based violence. In April 2009, in Sindh province, a minority minister stated that 18 Hindu women had been forced to convert to Islam. A month later, a Christian woman was abducted, raped and forced to convert to Islam, according to the 2009 USCIRF report.

Unidentified gunmen shot and wounded Pakistan's Religious Affairs Minister, Hamid Saeed Kazmi, in Karachi in September. Kazmi, a cleric and vocal opponent of the Taliban, belongs to the Barelvi sect – moderate adherents of Sufism.

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