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The Church of St. Anne stands in the Old Town of Vilnius, on the left bank of Vilnia River.

The church has a late Gothic period style, a rectangular shape, two towers and a three-sided apse. It is a single-nave building. Its presbytery and nave are covered with mesh vaults. A neo-Gothic brick bell tower stands by the church. It is connected to the church through a brick fence.

The Church of St. Anne is one of the most beautiful and, probably, one of the most famous buildings in Vilnius. It is a masterpiece of the late Gothic period. The church is shrouded in many legends. Popular legend has it that Napoleon visited Vilnius while travelling from Russia and was so fascinated by the beauty of the church that he said he wanted to take it back to Paris, if only this was possible. Unfortunately, the reality is not that romantic: during his march through Lithuania, Napoleon did not restrain his generals and soldiers who barbarically destroyed the church's wooden interior inventory.

The first Church of St. Anne in Vilnius was mentioned in 1495. It stood on the northern slope of Gediminas Castle Hill and belonged to the Franciscans. The church was destroyed in 1551 under the order of the Grand Duke Žygimantas Augustas, and a single-nave Church of St. Anne and Barbora was built in its place. It it believed that this church was designed by architect Džiovanis Činis. The church was of Renaissance style. It remained unfinished after the death of Žygimantas Augustas, and was damaged in 1655, as well as fully destroyed in 1666. Nowadays, the slabs of the foundations of former churches are placed here.

The current Church of St. Anne was built near Bernardinai monastery in 1495–1501. Pope Alexander VI declared a feast day for the church in 1501. According to the art historian D. Kačmažikas, the church was designed and built by Mykolas Enkingeris. From afar, it resembles a man kneeling for a prayer and raising his hands, and upon further inspection the main facade has the form of the Pillars of Gediminas. 33 different forms of bricks were used in the construction of the Church of St. Anne.

The church burned in 1560, 1564 and 1610, and was ravaged during the war in 1655. After the war, the interior of the church was plastered and whitened, and Baroque altars were installed. The church was restored after the fires of the 16th–17th centuries, and the exterior of the church that we see today remains almost unchanged. Even though it was restored several times, all of the masters tried to rebuild the former forms of the church as accurately as possible.

In June of 1941, two aviation bombs were dropped near the Church of St. Anne. In July of 1944, a water station was blown away in the neighbourhood of the church and grenade launchers dislocated nearby were shooting for three days and nights.

In 2009–2010, the roof of the church was replaced, facade elements were reinforced, and towers that once stood on the side facade abutments were restored.