- Christian minority member Fanish Masih, aged 19, was found dead on 15 September in Sialkot prison where he had been held in solitary confinement. Prison authorities claimed that he had committed suicide but his relatives reportedly noted bruises consistent with torture on his forehead, arms and legs. Three prison officials were suspended for negligence, but no criminal charges were brought against them.
- More than 250 bodies of suspected militants were reportedly found in Swat after mid-July, some hanging from poles, warning the Taleban of the same fate.
New instances of enforced disappearances were reported. Despite the resumption of Supreme Court hearings of disappearance cases in November, the fate and whereabouts of hundreds of disappeared people remained unknown.
- In October, a district court in Abbottabad declared former President Musharraf a suspect in the case of the alleged abduction of Atiq-ur Rehman, a scientist at the Pakistan Atomic Energy Commission, who disappeared on 25 June 2004.
- On 18 August, the army stated it was holding 900 prisoners arrested in Swat who would be handed over to relevant agencies. Their identity, whereabouts and fate remained unknown.
- On 3 April, three Baloch activists, Ghulam Mohammad Baloch, Lala Muni, and Sher Mohammad Baloch, were abducted by men in civilian clothing from their lawyer's office on the very day that the antiterrorism court cleared them of charges of causing unrest. They were reportedly taken away in Frontier Corps vehicles. They were found dead on 8 April. Ghulam Mohammad Baloch was a member of a committee to ascertain the identity of some 800 victims of enforced disappearance. The Balochistan High Court set up a judicial inquiry in April, and in September called on the intelligence agencies to assist the investigation of the murders after police had complained about their lack of co-operation.
Zakir Majeed Baloch, a social worker and vice chairman of the Baloch Students Organization, was according to family members picked up on 8 June by intelligence agency personnel near Mastung, Balochistan. Police refused to register the family's complaint. His fate and whereabouts remain unknown.
Discrimination - religious minorities
Members of religious minorities suffered increasing abuses, including abduction, murder, intimidation, and harassment, as state officials failed to protect them and adequately prosecute perpetrators. The Taleban imposed jizia, a tax payable by non-Muslims living under Muslim rule, on Sikhs, Hindus and Christians, or in some cases expelled them outright. Sectarian violence between the Sunni and Shi'a communities increased in Kurram Agency as Sunni Taleban exerted their control.
- At least 14 members of the Ahmadiyya community, including children, were arrested on charges of blasphemy which carries the mandatory death penalty. At least 11 Ahmadis and nine Christians were killed for their faith in separate incidents.
- On 29 January, five Ahmadis, including one minor, were detained on spurious charges of blasphemy in Layyah district, Punjab Province, with no evidence or witnesses to support the charges against them. They were released on bail.
- In Gojra, Punjab, over 1,000 people attacked the Christian quarter on 1 August, burning six people alive, including a seven-year-old child. Seventeen others were injured, one of whom died later. The attack was a response to rumours that Christians had torn pages of the Qur'an in neighbouring Korian. A judicial inquiry, ordered by the Punjab Chief Minister, submitted its findings to Punjab authorities in early September; they were not made public. Of 42 people arrested on charges stemming from the attack in Gojra, 35 were released on bail.
Violence against women and girls
Women continued to be victims of "honour killings", with 960 incidents reported. In September, the Punjab law minister announced that crimes against women would be tried under the Anti-Terrorism Act.