During the Sąjūdis period, many civil initiatives came from grass-roots organisations and the patriotic underground. One such initiative was to find out, collect, investigate and disseminate information about the crimes of the Soviet regime. Various non-governmental organisations started to study Stalinist crimes and the history of the resistance and the Lithuanian partisan movement. In 1992, the Lithuanian parliament established the State Residents’ Genocide Centre of Lithuania (VLGGTC), which sought to combine these organisations and activities, providing state direction and funding. The centre was assigned the task of preserving, handling and studying archives of special significance.

In 1993, the VLGGTC was reorganised into the Genocide and Resistance Research Centre of Lithuania (LGGRTC), comprising two institutes: the Lithuanian Genocide and Resistance Research Institute, and the Lithuanian Genocide Victims Remembrance Institute. Vytautas Skuodis, an anti-Soviet resistance activist and underground publisher, was appointed director of the centre. In 1994, the Commission for the Rights of Participants in the Resistance Movement was merged with the LGGRTC, and the centre was assigned the task of issuing IDs to those who had participated in the resistance.
In 1997, the LGGRTC was expanded, to include the Centre for the Research of Repression in Lithuania (which began operating in 1992 at the Lithuanian Institute of Philosophy, Sociology and Law), and the Lithuanian Museum of Genocide Victims (which began operating in October 1992 in the former KGB building).

In 1998, the Foundation for Lithuanian Genocide and Resistance Research and Victim Support and Remembrance was established within the framework of the LGGRTC. The foundation provides financial assistance to participants in the resistance movement and victims of repressions, and finances key remembrance programmes.