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The largest religious group in Bavaria is Roman Catholic (ca. 67%), followed by Lutheran Protestants (23%). The state's Muslim population is mainly from Turkey, and currently has 8 mosques and around 40 houses of prayer to celebrate its services. During the Middle Ages, Jews lived in almost all Bavaria's towns and markets, as well as in the countryside. From the 14th century onwards, they were subjected to several pogroms. After being deprived of their rights and citizenship, Jews living in Nazi Germany were deported and murdered - and today Jews make up a religious minority of just 1.0%. Their numbers are increasing, however, due to a recent influx of immigrants from the regions previously occupied by the former Soviet Union.

Catholics, Lutherans and Jews were only accorded equal civil rights in the 19th century. Beforehand, a person's religion used to depend on that of the local prince, who also had the power to decide whether other religions would be tolerated or not.