The Lithuanian Revival Movement, Sąjūdis, was founded on 3 June 1988. In July, the first commission for research into Stalinist crimes, led by Professor Julius Juzeliūnas, was set up. A group led by Mečys Laurinkus sent out questionnaires about deportations of Lithuanians, hard labour camps and killings, which were later systematised and catalogued.

On 25 September 1991, a working group, led by Balys Gajauskas, was founded in the Supreme Council of the Lithuanian Republic to work with documents dealing with KGB activities in Lithuania.

On 29 October 1992, the Supreme Council of the Lithuanian Republic founded the State Genocide Research Centre of Lithuania. On 26 November 1992 the Lithuanian government approved the centre’s provisional regulations, appointing Juozas Starkauskas its acting head.

In October 1992, the Lithuanian Museum of Genocide Victims opened under the Ministry of Culture. Gintaras Vaičiūnas was its first director.

On 16 July 1993, the Seimas passed the Law on the Genocide and Resistance Research Centre of Lithuania. On that day the working group dealing with documents about the activities of the KGB in Lithuania was reorganised. The State Genocide Research Centre of Lithuania was reorganised into the Genocide and Resistance Research Centre of Lithuania, consisting of the Lithuanian Genocide and Resistance Research Institute and the Lithuanian Genocide Victims Memorial Institute. On 17 February 1994 the Seimas appointed Vytautas Skuodis general director of the newly established centre

On 28 December 1993, the Research Centre for the Reprisals in Lithuania was founded at the Lithuanian Institute of Philosophy, Sociology and Law, with Birutė Burauskaitė as its head.

On 20 July 1994, the Aid Foundation for Genocide and Resistance Victims was set up, with Stasys Stungurys as its head. On 7 April 1998,  it was reorganised into the Lithuanian Genocide and Resistance Research, Victim Support and Immortalisation Foundation. Povilas Jakučionis was appointed chairman of the board. Since 18 August 2000,  Jonas Valenčius has been chairman of the board.

On 17 November 1994, the Seimas voted to join the Resistance Participants’ Rights Commission with Povilas Varanauskas as its head, to the centre. On 13 February 1997, the Seimas passed the Law on the Organisation of the Centre, and dismissed Skuodis from the post of general director, appointing Dalia Kuodytė to the post on 18 February. Observing the Law on the Reorganisation of the Centre, on 24 March 1997, the Lithuanian government transferred the Research Centre for Reprisals in Lithuania and the Museum of Genocide Victims (director Eugenijus Peikštenis) to the centre.

On 5 June 1997, the Seimas passed the Law on the Centre, and on 11 November 1997, it passed the centre’s regulations.

The Genocide and Resistance Research Centre of Lithuania is a state institution which investigates all manifestations of genocide and crimes against humanity, the persecution during the Soviet and Nazi occupations, and the armed and peaceful resistance to the occupations. It also gives juridical evaluations of the perpetrators of the reprisals and genocide, and immortalises the memory of the freedom fighters and genocide victims.

The objectives of the centre are to establish historical truth and justice; to investigate the physical and spiritual genocide of Lithuanians carried out by the occupying regimes between 1939 and 1990, and the resistance to the regimes; to immortalise the memory of the freedom fighters and the genocide victims; and to initiate the juridical evaluation of the aftermath of the occupying regimes. The centre also researches into the policy of the occupying regime in the Vilnius district from 1920 to 1939 and the processes of resistance to it.