East Timor (Timor-Leste) was occupied by Indonesian forces just days after declaring independence from Portugal in November 1975. Over the next 25 years, human rights violations were widespread.

In 1999 an overwhelming majority of the population voted for independence from Indonesia in a UN-supervised referendum. In the weeks that followed, anti-independence militia supported by the Indonesian military conducted a campaign in which 1,400 were killed and 300,000 were displaced.

East Timor became a sovereign state on May 20, 2002 and has enjoyed relative stability ever since. UN forces were deployed in 2006 to help quell an army mutiny, but were withdrawn in 2011.

In 2011 a United Nations Working Group on Enforced or Involuntary Disappearances quoted the East Timor Commission for Reception, Truth and Reconciliation figure of at least 102,800 civilian casualties – from violence, illness or hunger – during the Indonesian occupation 1975-1999, including 18,600 killed or disappeared. Other organizations put the casualty figures even higher and the number of missing in the tens of thousands.

The Victorian Institute of Forensic Medicine (VIFM) and the Argentine Forensic Anthropology Team (EAAF) signed a memorandum of understanding to form the International Forensic Team (IFT), which was invited by the Government of Timor-Leste to undertake exhumations at several mass grave sites, but countrywide a relatively small number of remains have been located and identified so far.

The International Committee of the Red Cross (ICRC) has been gathering reports of missing persons from family members in East Timor and presenting them to the authorities since 1979. Follow up has been minimal.

The International Stability Journal reports on the fitful progress of steps to locate and identify the missing and to organize a strategic approach to confronting the issues of responsibility and memory. Efforts to establish a Commission on Missing Persons have been bogged down in political disagreement, and In March 2012 parliament voted to defer the establishment of an Institute for Memory, which would have included a Centre for Victim Identification.

Efforts to prosecute perpetrators have also been limited. As of March 2013 only 27 individuals suspected of committing enforced disappearance had been indicted.