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Throughout the civil war in Afghanistan, the Northern Alliance committed a wide range of human rights abuses, ranging from systematic targeted killings, assassinations and rapes to forced disappearances and kidnappings. Created as a military-political umbrella organization in late 1996 under the the leadership of Ahmad Shah Massoud to resist the ruling Taliban regime, the Northern Alliance was ethnically dominated by the Tajik minority ethnic group of Afghanistan, as well as smaller numbers of Hazaras, Uzbeks and Turkmen as opposed to the Taliban who were Pashtun-dominated.

Human Rights Watch
During the United States-led coalition's invasion of Afghanistan in 2001, the United States was reluctant to pledge its full support to the Northern Alliance, the main Afghan opposition faction, because of concerns over human rights abuses perpetrated by the group. A Human Rights Watch (HRW) report warned in a report against providing military support to the Northern Alliance, citing the group of having involvement in killings, discriminate aerial bombardment, direct attacks on civilians and summary executions.

The report pointed out the alleged systematic abuse of ethnic Pashtuns in Sangcharak in northern Afghanistan between 1999 and 2000, during the Northern Alliance's four month long occupation of the region. In March 1995, mass rape and looting took place in a Hazara neighbourhood in Kabul by Masood's Jamiat forces. In May 1997, Northern Alliance General Abdul Malik's forces carried out brutual executions of 3,000 prisoners after an unsuccessful Taliban attack on the town of Mazar-e-Sharif. During September 1998, Masood's forces were believed to have bombed civilian areas in the north of Kabul, in which up to 180 people were killed.

The HRW noted in the report that not a single Northern Alliance commander had been brought to account for the human rights abuses in the country, and feared that the faction would carry out more human rights abuses when given the opportunity.