The issue of Polish and Lithuanian relations during the World War II is a controversial one, and some modern Lithuanian and Polish historians still differ in their interpretations of the related events, many of which are related to the Lithuanian collaboration with Nazi Germany and the operations of Polish resistance organization of Armia Krajowa on territories inhabited by Lithuanians and Poles. Several common academic conferences started bridging the gap between Lithuanian and Polish interpretations, but significant differences remain.

Background Polish–Lithuanian relations were strained during the interwar period, mostly due to the conflict over the Vilnius Region (which had a Polish majority but was seen by Lithuanians as their historical capital).Michael MacQueen, The Context of Mass Destruction: Agents and Prerequisites of the Holocaust in Lithuania, Holocaust and Genocide Studies, Volume 12, Number 1, pp. 27-48, 1998, This conflict resulted in enmity within local communities and the mutual harsh treatment of the Polish and Lithuanian ethnic minorities living in both countries. The tensions had begun to diminish by early spring of 1938 (see 1938 Polish ultimatum to Lithuania), when both nations restored normal relations, and telephone, mail, rail, and road communications were established.A study of crisis By Michael Brecher, Jonathan Wilkenfeld, page 255 "This was followed by a period of relative harmony between the two states The rapprochement was however stopped when Germany invaded Poland on the first day of September 1939. Germany had proposed Lithuania join in the invasion to gain control of the disputed Vilnius Region. However, despite Lithuania's antipathy towards Poland, the Lithuanian government was distrustful of Germany and refused. Lithuania thus remained neutral and independent in the initial days of World War II.

On September 17, the Soviet invasion of Poland began following its Molotov-Ribbentrop Pact. The Vilnius Region was soon occupied by the Red Army, which intended to place it inside the borders of the Belarusian Soviet Socialist Republic. On September 19, Lithuanian envoy in Moscow Ladas Natkevičius claimed Lithuanian rights to Vilnius, which was now occupied by the Red Army and was out of Polish control. After the new German-Soviet border was established on September 28, the Soviets invited the Lithuanians to talks. Negotiations lasted from October 3 to 10. The result of the talks was the "Treaty on Mutual Assistance and Transfer of Vilnius and Vilnius Region to Lithuania," under which, in exchange for Vilnius, Lithuania agreed to establish Soviet military bases on its territory. The agreement came as a result of immense Soviet pressure, and Lithuanian diplomats had no illusions that the presence of Soviet troops meant preparation for annexation. During negotiations, the Soviets threatened the possibility of annexing Vilnius to Soviet Belarus, and even the possibility of reconstituting the Lithuanian-Belarusian SSR.

The Polish envoy in Kaunas, Franciszek Charwat, submitted a protest note on behalf of the Polish government. The Lithuanian side responded that Vilnius was and is an inseparable part of Lithuania, which Poland occupied since 1920. According to Polish military attaché , the Lithuanians' response was even harsher, they were to state that they did not recognize the Polish government in Paris and for them Poland ceased to exist. In response, Charwat left Lithuania, thus officially breaking off Polish-Lithuanian relations and restarting a strong feeling of hostility between the two countries. Nevertheless, the pressing matter for Lithuania now became resisting Soviet pressure: most of the better politically oriented Lithuanian intelligentsia realized that the takeover of the Vilnius region was merely a prelude to the occupation of Lithuania by Soviet forces. Ultimately, on 15 June, the Red Army invaded Lithuania, soon followed up by invasions of the two other Baltic States, Latvia and Estonia. On 3 August, Lithuania was formally annexed to the USSR as the Lithuanian Socialist Soviet Republic.Breslavskienė L, Lietuvos okupacija ir aneksija 1939-1940: dokumentų rinkinys, Vilnius: Mintis, 1993. Lithuania remained under the Soviet Union for nearly a year, until on 22 June 1941, Nazi Germany began an invasion of the Soviet Union and crossed the border into Lithuania, thereafter occupying it.

Conflicting ideologies The Vilnius Region had a complex demographic history. This was further aggravated by Germans forcibly relocating Lithuanian families to the region from western parts of Lithuania.

A significant number of Lithuanians started collaborating with the German occupiers,Piotrowski, 1998, p.163Snyder, p.84Alvydas Nikžentaitis, Stefan Schreiner, Darius Staliunas, The Vanished World of Lithuanian Jews, Rodopi, 2004, ,Google Print, p.3Leonidas Donskis, Identity and Freedom: mapping nationalism and social criticism in twentieth-century Lithuania, Routledge, 2002, , Google Print, p.74 a prominent example being the Lithuanian Activist Front, many members of whom came from the National Unionists whose pre-war slogan was 'Lithuania for Lithuanians'. The Lithuanian government, encouraged by the Germans, hoped that the Germans would grant Lithuania as much autonomy as it has granted Slovakia. Even through LAF faded after 1941, and Germans never granted the Lithuanians the autonomy they desired, elements within the Lithuanian government, collaborating with Germans, engaged in the program of ethnic and racial purification, targeting Jews, Poles and other non-Lithuanian ethnic minorities.Snyder, p.82 Anti-Polish rhetoric and violence became common under the Juozas Ambrazevičius government in 1941 (followed by the role of Petras Kubiliūnas as a puppet counsel to the German rulers).Piotrowski, 1998 Kubiliūnas led the puppet-Council advising the German government of the "general District Lithuania" (Generalbezirk Litauen) led by Generalkommissar of Lithuania Theodor Adrian von Renteln. Some Lithuanian clergy called for pogroms of Poles, stating that the Poles were worse than the Jews and offered indulgences for killing Poles. A Lithuanian professor wrote a pamphlet on "Why Should we hate the Poles", and LAF campaigned for the establishment of ghettos for Poles, requirement for them to wear identifying badges, and reduction of their food rations, claiming that "under Soviets, we killed 50% of Poles, under Germans we will kill the other 50%". One of the most infamous series of incidents took place in the Paneriai () district of Vilnius, where from 1941 to 1943 Germans and Lithuanians massacred tens of thousands of Jews and Poles.Kazimierz Sakowicz, Yitzhak Arad, Ponary Diary, 1941-1943: A Bystander's Account of a Mass Murder, Yale University Press, 2005, , Google Print.Piotrowski, 1998, p.168

Around 1943, one of the political factions of the Government Delegation for Poland for the Vilnius region, the Vilnius Democratic Concentration () – the underground union of leftist Polish parties, Piotr Niwiński, Okręgowa Delegatura Rządu w Wilnie partly because of the pro-Nazi stance of Lithuanian authorities, and partly influenced by the nationalist stance of Polish Endecja party, stated a plan to occupy Lithuania after the war, submit it under the rule of Polish General Commissariat and to re-educate "corrupt" Lithuanians. Arūnas Bubnys. Armijos Krajovos ištakos ir ideologija Lietuvoje (Beginnings and ideology of Armia Krajowa in Lithuania). Armija Krajova Lietuvoje, pp. 6-13. A. Bubnys, K. Garšva, E. Gečiauskas, J. Lebionka, J. Saudargienė, R. Zizas (editors). Vilnius – Kaunas, 1995. On 1 March 1944, the Polish issued declaration expressing preparation to fight for Eastern Borderlands (Vilnius, Grodno, Lviv, Lida, Novogrudok, and Pinsk). However, such declarations of local Polish politicians differed significantly from the official statement and actions of the Polish government-in-exile, which was the only country among the anti-Nazi coalition which declared its support for the cause of Lithuanian post-war independence.Antypolski film w litewskiej telewizji. Article from Rzeczpospolita reprinted on the pages by Polish Ministry of Foreign Affairs.. Anna Pisarczyk, Wyboista droga do pojednania, "MAGAZYN WILEŃSKI", 4/2006

Although Lithuanian and Polish resistance movements had common enemies – Nazi Germany and the Soviet Union – they never became allies. The main obstacle in allying was the question of Vilnius – the Polish government in exile and the Polish resistance regarded Vilnius as part of Poland, while Lithuanian resistance regarded Vilnius as the capital of Lithuania. Lithuanian resistance saw the Soviet Union as the main enemy and Nazi Germany as its secondary enemy. Polish resistance saw Nazi Germany as the main enemy and was much more ambiguous on the Soviet Union. Only in 1944–1945, after the Soviet reoccupation, did Lithuanian and Polish resistance start cooperating in the fight against the Soviets. Arūnas Bubnys. Lietuvių ir lenkų pasipriešinimo judėjimai 1942–1945 m.: sąsajos ir skirtumai (Lithuanian and Polish resistance movements 1942-1945), 30 January 2004

Armed conflict

Lithuanian authorities had been aiding Germans in their actions against Poles since the very beginning of German occupation in 1941, which resulted in the deaths of thousands of Poles. Thousands of Poles were killed by Lithuanian collaborators working with Nazis (like the German subordinated Lithuanian Security Police Gazeta Wyborcza, 2001-02-14, Litewska prokuratura przesłuchuje weteranów AK (Lithuanian prosecutor questioning AK veterans), last accessed on 7 June 2006] or the Lithuanian Territorial Defense Force under the command of general Povilas Plechavičius, Gazeta Wyborcza, 2004-09-01, W Wilnie pojednają się dziś weterani litewskiej armii i polskiej AK (Today in Vilnius veterans of Lithuanian army and AK will forgive each other), last accessed on 7 June 2006 many more were deported into Germany as slave labour.Piotrowski, p.168, p.169) Tadeusz Piotrowski notes that thousands of Poles died at the hand of Lithuanian collaborators, and tens of thousands were deported. In autumn 1943, Armia Krajowa started operations against the Lithuanian collaborative organization, the Lithuanian Security Police, which had been aiding Germans in their operation since its very creation. Polish political and military underground cells were created all over Lithuania, Polish partisan attacks were usually not only in Vilnius Region but across the former demarcation line as well. Soon a significant proportion of AK operations became directed against Nazi Germany allied Lithuanian Police and local Lithuanian administration. During the first half of 1944 AK killed hundreds of Lithuanians serving in Nazi auxiliary units or organizations: policemen, members of village self-defence units, servants of local administration, soldiers of the Lithuanian Territorial Defense Force and other Nazi collaborators. Civilians on both sides increasingly numbered among the casualties. Arūnas Bubnys. Armija Krajova Rytų Lietuvoje (Armia Krajowa in Eastern Lithuania). "Atgimimas", 9 June 1989, No. 22 (35)