Since 1979 Afghanistan has been in a state of conflict that has left hundreds of thousands missing or displaced. The Soviet intervention in 1979 to support a pro-communist regime led to a decade-long war with guerrilla mujahideen, supported by the United States, Saudi Arabia and Pakistan. Following the Soviet withdrawal civil war continued, and in late 2001 a US-led invasion toppled the Taliban. From August 2003, the NATO-led International Security Assistance Force (ISAF) conducted security operations while training and developing the Afghan National Security Forces (ANSF). Afghanistan had its first democratic presidential election since the fall of the Taliban in June 2014, with NATO troops scheduled to leave by the end of 2014.

A 2012 report by the Afghanistan Independent Human Rights Commission (AIHRC) found that over a million people were killed and 1.3 million injured or disabled in 35 years of conflict. An estimated 1 million of those are missing or disappeared. The AIHRC report presents evidence of no fewer than 180 mass graves and of systematic mass slaughter by the both Taliban and opposition groups.

The Afghan authorities lack the capabilities to effectively locate the missing and to identify their remains. There is evidence of graves being destroyed by those wishing to cover up crimes. In December 2008, amid concerns about a reported excavation at a mass grave site in northern Afghanistan, a senior UN official reiterated that the organization is committed to helping Afghan authorities preserve such sites in order to protect evidence of crimes committed over the 35 years of war. A spokesman for the UN Assistance Mission for Afghanistan (UNAMA) said the UN would provide assistance to enable Afghans to uncover past crimes and identify victims.

With the backing of the UN and Physicians for Human Rights, the Afghanistan Forensic Science Organization (AFSO) was established in Kabul in March 2012. The AFSO is the first non-governmental forensic science organization in Afghanistan. Its mission is to document and protect the integrity of six mass graves in three different provinces and to raise awareness about the importance of documenting mass graves in the country at large.

The Bonn Agreement that led to the establishment of the Transitional Authority in Afghanistan in 2001 did not address war crimes or the issue of missing persons, and U.S. and NATO forces initially concentrated on fighting terrorism.

The Afghan Government says the National Reconciliation, General Amnesty and Stability Law of 2010 will enhance reconciliation and stability. Critics, however, argue that the law grants immunity to those who have violated human rights, often on a large scale. The International Centre for Transitional Justice (ICTJ), which has worked in Afghanistan since 2002, says: Blanket amnesties promote impunity and are currently deemed unlawful under international law.”