The Church of St. Francis Xavier stands on Rotušės square in the Old Town of Kaunas. The Jesuits opened a residence here in 1642 and a chapel in 1643, founded a primary school in 1649, and began the stone church in 1666. Pranciškus Milvydas led the construction. The Baroque church was finished in 1720, and its towers were completed in 1725. A fire in 1732 caused the roof and a tower to collapse, and the tower was rebuilt from 1746 to 1751.
By the late eighteenth century the church had twelve Baroque altars. The Jesuits left after 1773, the Franciscans received the church in 1787, and Russian authorities closed it in 1812. It became Orthodox in 1842, and its altars were demolished.
It was closed in 1949 and converted into a sports hall. The church returned to the Jesuits in 1990 and was reconsecrated on August 30, 1992.

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