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In the 16th century, a Gothic chapel of the Holy Cross was built by the Bishop of Vilnius Povilas Alšėniškis. Soon, a residential house next to it was converted into a Baroque church which was given to the Bonifrati. Bonifrati monks settled in this church and fulfilled their task of treating the sick. The Bonifrati church was famous for the well in its cellar which produced miraculous healing water, and the miraculous painting of St. Mary Snow (Bonifrati Mother of God) on the high altar.
An abbey house was built together with the original church. A chapel built by Povilas Alšėniškis in 1543 was incorporated in its eastern part. A new block was built in the western part with a spacious infirmary hall connected to the entryway of the church.
Two brick towers were built instead of one in 1725. The church is small, with modest forms, thus it is different from other churches which have a splendid Baroque style. After the fire of 1737, a curved contour pediment was inserted between the towers, altars were built, and a utilitarian entryway with a one-sided roof was added to the main facade. Later, after the fire of 1748, the altars and the tower helmets were remade to have late Baroque style forms. The church is rectangular, single-nave with a presbytery and sacristy which do not stand out from the seamless space. The upper tiers of the towers are decorated with blades, finished with Rococo-style helmets, with oval windows and ornamented crosses. The most valuable interior of the church was heavily decorated in 1749–1754.
In 1976, new organs were installed and an organ and chamber music concert hall was built in the church, also known as the Small Baroque Hall. Nowadays, the Church has been returned to the faithful and holds masses in the Lithuanian language.