In 1944, when the Soviet Union occupied Lithuania for the second time, tens of thousands of Lithuanian patriots joined the struggle against the occupation authorities. In 1944–1945, about 30,000 armed men joined forces in the forests. Some of them joined the partisans to avoid serving in the occupation army, others to avoid possible reprisals or deportation. However, the majority chose armed struggle consciously and were committed to fighting until the restoration of an independent Lithuanian state. In autumn 1944, small partisan groups started forming larger units, and subsequently – districts. A district consisted of 2–5 brigades and these were subdivided into companies (tėvūnija [a partisan unit, which operated in several rural areas]), squads, and units. A region comprised 2–3 districts. Partisan groups regulated their activities with statutes and rules. Those who joined the partisans took an oath. Partisans wore military uniforms with insignia.
In 1949, despite the weakening of the partisan resistance, partisans continued to fight actively, managed to unite Lithuanian patriotic forces into one organisation, and formed a joint military and political leadership of resistance. At the meeting of Lithuania’s partisan commanders in February 1949, the Movement for the Struggle for Freedom of Lithuania (LLKS) was established and military and political documents were adopted. On 16 February 1949, LLKS issued a political declaration, which proclaimed that the supreme legitimate authority in Lithuania was the partisan leadership, and the aim of their fight was to restore an independent democratic Republic of Lithuania. Captain Jonas Žemaitis-Vytautas of the Lithuanian Army was elected the chairman of the presidium of the LLKS Council.
The 10 years of resistance, also known as the Lithuanian War, resistance or partisan war, is exceptional in the history of Lithuania from several aspects: duration (almost 10 years), universality (during the entire period there were at least 50,000 active members of the armed resistance and about 100,000 others who participated in the resistance as members of the underground organisations and supporters), and the unequal balance of power which was unfavourable to the Lithuanian partisans. Over 20,000 partisans perished in this war.
The main research directions of this programme are causes of the war, activities and organisational structure of individual partisan regions, partisan documents and printing, establishment and activities of the senior command, the structure of the military repressive occupation authorities in Lithuania and their activities which were aimed at destroying the armed resistance.
- Juozas Starkauskas, Čekistinė kariuomenė Lietuvoje 1944–1953 metais (NKVD–MVD–MGB kariuomenė partizaninio karo laikotarpiu) [The Chekist Army in Lithuania in 1944–1953, the NKVD-MVD-MGB Army during the Partisan War], 1998
- Partizanai apie pasaulį, politiką ir save (1944–1956 m. partizanų spaudos publikacijos) [The Partisans about the World, Politics and Themselves; The Publications of the Partisans’ Press in 1944–1956], compiled by Nijolė Gaškaitė-Žemaitienė, 1998
- Nijolė Gaškaitė-Žemaitienė, Žuvusiųjų prezidentas. Jono Žemaičio biografija (The President of the Perished. The Biography of Jonas Žemaitis), 1998, 2005, 2007, 2009
- Juozas Starkauskas, Stribai (Ginkluotieji kolaborantai Lietuvoje partizaninio karo laikotarpiu, 1944–1953) [The Stribai: the Armed Collaborators during the Partisan war in Lithuania in 1944–1953], 2001
- The Anti-Soviet Resistance in the Baltic States, 1999, 2000, 2001, 2002, 2006
- Pilietinis pasipriešinimas Lietuvoje ir Lenkijoje: sąsajos ir ypatumai, 1939–1956 [The Civil Resistance in Lithuania and Poland in 1939–1956: Connections and Specifics], edited by Arvydas Anušauskas, 2004
- Rokas Tracevskis, Dalia Kuodytė, The Unknown War. Armed anti-Soviet resistance in Lithuania in 1944–1953 [in English], 2004, 2005, 2006, 2013
- Juozas Starkauskas. Represinių struktūrų ir komunistų partijos bendradarbiavimas įtvirtinant okupacinį režimą Lietuvoje 1944–1953 m. [The Co-operation of Secret Services and the Communist Party Imposing the Soviet Occupational Regime in Lithuania in 1944–1953], 2007
- Rokas Tracevskis, Dalia Kuodytė, Tuntematon sota - Liettuan neuvostovastainen aseistettuvastarinta vuosina 1944-1953 [in Finnish], Veterator Oy, 2007
- Pietų Lietuvos partizanų sritis. Atlasas [The Partisan Region of Southern Lithuania. The Atlas], 2008
- Vakarų Lietuvos partizanų sritis. Atlasas [The Partsian Region of Western Lithuania. The Atlas], compiled by Edita Jankauskienė, Rūta Trimonienė and Dalius Žygelis, 2010
- Partizano keliu [The Partisan Way], compiled by Aurelija Malinauskaitė and Darius Juodis, 2012
- Rokas Tracevskis, The Manor of Horror: the Soviet-Era Mass Grave in Vilnius [in English], 2013
- Rokas Tracevskis, Dalia Kuodytė, La Guerra Sconosciuta. La resistenza armata antisovietica in Lituania negli anni 1944-1953 [in Italian], Il Cerchio, 2014, 2015