The predominantly East Slavic population of the Grand Duchy was mostly Eastern Orthodox, and much of the Lithuanian state's nobility also remained Orthodox. Unlike the common people of the Lithuanian realm, at about the time of the Union of Lublin in 1569 large portions of the nobility converted to Western Christianity. Following the Protestant Reformation movement, many noble families converted to Calvinism in the 1550s and 1560s, and typically a generation later, conforming to the Counter-Reformation trends in the Commonwealth, to Roman Catholicism. The Protestant and Orthodox presence must have been very strong, because according to an undoubtedly exaggerated early 17th-century source, "merely one in a thousand remained a Catholic" in Lithuania at that time. In the early Commonwealth, religious toleration was the norm and was officially enacted by the Warsaw Confederation in 1573.
By 1750, nominal Catholics comprised about 80% of the Commonwealth's population, the vast majority of the noble citizenry, and the entire legislature. In the east, there were also the Eastern Orthodox Church adherents. However, Catholics in the Grand Duchy itself were split. Under half were Latin rite with strong allegiance to Rome. The others (mostly non-noble Ruthenians) followed the Eastern rite. They were the so-called Uniates, whose church was established at the Union of Brest in 1596, and they acknowledged only nominal obedience to Rome. At first the advantage went to the advancing Roman Catholic Church pushing back a retreating Orthodox Church. However, after the first partition of the Commonwealth in 1772, the Orthodox had the support of the government and gained the upper hand. The Russian Orthodox Church paid special attention to the Uniates (who had once been Orthodox), and tried to bring them back. The contest was political and spiritual, utilizing missionaries, schools, and pressure exerted by powerful nobles and landlords. By 1800, over 2 million of the Uniates had become Orthodox, and another 1.6 million by 1839.
On June 22, 1941, Nazi Germany invaded the Soviet Union in Operation Barbarossa. The German forces moved rapidly and encountered only sporadic Soviet resistance. Vilnius was captured on June 24, 1941, and Germany controlled all of Lithuania within a week. The retreating Soviet forces murdered between 1,000 and 1,500 people, mostly ethnic Lithuanians (see Rainiai massacre). The Lithuanians generally greeted the Germans as liberators from the oppressive Soviet regime and hoped that Germany would restore some autonomy to their country. The Lithuanian Activist Front organized an anti-Soviet revolt known as the June Uprising in Lithuania, declared independence, and formed a Provisional Government of Lithuania with Juozas Ambrazeviius as prime minister. The Provisional Government was not forcibly dissolved; stripped by the Germans of any actual power, it resigned on August 5, 1941. Germany established the civil administration known as the Reichskommissariat Ostland.
Initially, there was substantial cooperation and collaboration between the German forces and some Lithuanians. Lithuanians joined the Tautinio Darbo Apsaugos Batalionas (TDA) and Schutzmannschaft police battalions in hopes that these police units would be later transformed into the regular army of independent Lithuania. Instead, these units were employed by the Germans as auxiliaries in perpetrating the Holocaust. However, soon Lithuanians became disillusioned with harsh German policies of collecting large war provisions, gathering people for forced labor in Germany, conscripting men into the German army, and the lack of true autonomy. These feelings only naturally led to the creation of a resistance movement. The most notable resistance organization, the Supreme Committee for the Liberation of Lithuania, was formed in 1943. Due to passive resistance, a Waffen-SS division was not established in Lithuania. As a compromise, the Lithuanian general Povilas Plechaviius formed the short-lived Lithuanian Territorial Defense Force (LTDF). Lithuanians did not organize armed resistance, still considering Soviet Union their primary enemy. Armed resistance was conducted by pro-Soviet partisans (mainly Russians, Belarusians and Jews) and Polish Armia Krajowa (AK) in eastern Lithuania.
Before the Holocaust, Lithuania was home to a disputed number of Jews: 210,000 according to one estimate, 250,000 according to another. About 90% or more of the Lithuanian Jews were murdered, one of the highest rates in Europe. The Holocaust in Lithuania can be divided into three stages: mass executions (JuneDecember 1941), a ghetto period (1942 March 1943), and a final liquidation (April 1943 July 1944). Unlike in other Nazi-occupied countries where the Holocaust was introduced gradually, Einsatzgruppe A started executions in Lithuania on the first days of the German occupation. The executions were carried out by the Nazis and their Lithuanian collaborators in three main areas: Kaunas (marked by the Ninth Fort), in Vilnius (marked by the Ponary massacre), and in the countryside (sponsored by the Rollkommando Hamann). An estimated 80% of Lithuanian Jews were killed before 1942. The surviving 43,000 Jews were concentrated in the Vilnius Ghetto, Kaunas Ghetto, iauliai Ghetto, and venionys Ghetto and forced to work for the benefit of German military industry. In 1943, the ghettos were either liquidated or turned into concentration camps. Only about 2,0003,000 Lithuanian Jews were liberated from these camps. More survived by withdrawing into the interior of Russia before the war broke out or by escaping the ghettos and joining the Jewish partisans.