The museum was established in 1992 by order of the Minister of Culture and Education and the president of the Lithuanian Union of Political Prisoners and Deportees.

[1] The museum is dedicated mostly to collecting and exhibiting documents relating to the 50-year occupation of Lithuania by the Soviet Union, the anti-Soviet Lithuanian partisans, and the victims of the arrests, deportations, and executions that took place during this period.

[2] This definition has been accepted by the European Court of Human Rights in Lithuanian genocide convictions against Soviet occupation forces.

After independence was declared, it served as a conscription center for the newly formed Lithuanian army and as the Vilnius commander's headquarters.

A section devoted to the victims of deportations, arrests, and executions holds photographs, documents, and personal belongings; this collection is continually expanded by donations from the public, seeing the museum as the best means of preserving the materials.

[10] According to Time Magazine, the museum "focuses almost entirely on the murder of the Lithuanian non-Jewish population, while perpetrators of the Holocaust are lauded as victims in their countries’ struggle against Soviet occupation.