Islam has been in Lithuania a long time. It was so because the medieval Grand Duchy of Lithuania of the Polish–Lithuanian Commonwealth, stretching from Baltic to Black seas, included some Muslim lands in the south, inhabited by Crimean Tatars. Some of people from those lands were moved into ethnically Lithuanian lands, now the current Republic of Lithuania, mainly under rule of Grand Duke Vytautas. The Tatars, now referred to as Lithuanian Tatars, lost their language over time and now speak Lithuanian as natives; however, they have not lost Islam as their religion. Due to long isolation from all the other Islamic world, the practices of the Lithuanian Tatars differs somewhat from the rest of Sunni Muslims; they are not considered a separate sect however.

In Lithuania, unlike many other European societies at the time, religious freedom was pursued. Lithuanian Tatars settled in certain places, such as around Raižiai (in Alytus district municipality).

Much of the Lithuanian Tatar culture, mosques, graveyards and such were destroyed by the Soviet Union after it annexed Lithuania. After restoration of Lithuanian independence however the government supported the promotion of Lithuanian Tatar culture among those Lithuanian tatars who lost it. Three original wooden mosques remain now (in villages of Nemėžis, Keturiasdešimt Totorių (both in Vilnius district municipality) and Raižiai (Alytus district municipality), typically having relatively large Muslim populations), as well as a new brick mosque built in Kaunas during the period of interwar independence of Lithuania (in the 30s) to commemorate the anniversary of Vytautas, the duke who brought Tatars and Islam to Lithuania. That mosque is called Vytautas Didysis Mosque after the Grand Duke Vytautas. In the capital of Lithuania, Vilnius, however, no mosque remains, as Russians destroyed the Lukiškės Mosque which was there. The Lithuanian Tatar community is trying to rebuild the mosque, but faces various problems, including lack of funds as well as certain actions by the government of Vilnius city municipality.

Currently, only several thousand Lithuanian Tatars remain; however, with the restoration of Lithuanian independence, they are experiencing a kind of national revival.

During the time of the Soviet Union, some people from other Muslim nationalities were moved in, however many of them were atheists; as well other Muslims came as immigrants after restoration of independence, but as for now this number is very small compared to similar numbers in western Europe; therefore for now Lithuanian Tatars remain the core of Islam in Lithuania, supported by some Lithuanians who converted. Overall, there are less than 3000 Muslims in Lithuania according to the last census held in 2001.

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