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The Bernardine historical–architectural ensemble is a unique urban complex of Vilnius Old Town. In addition to the well-known Church of St. Francis of Assisi (Bernardine) and the Church of St. Anne, it also includes the Bernardine Monastery. 

The first Bernardine church in Vilnius was most likely wooden and was named after St. Bernardino of Siena (it burned down in 1475). In around 1490, the Bernardines built themselves a new brick church. However, in 1500, a large part of it had to be taken apart due to construction errors, since its foundation sunk, the walls had cracks, and its vaults began to fall apart. The old sacristy and presbytery – monk choir overlaid with a beautiful crystal vault were preserved the best since the construction of the 15th century.

The third church was built at the same location in 1506–1516 and consecrated under the name of St. Francis of Assisi. In the 16th century, travellers visiting Vilnius wrote about the new Bernardine Church describing it as one of the largest and most ornate buildings in the city.

Along with the Church of St. Anne built nearby in 1495–1500 and often called a chapel, the Bernardine ensemble of Vilnius could be distinguished by its greatness and splendour at the beginning of the 16th century. Its unique architecture was also highlighted by the location chosen for the convention – buildings situated on the outskirts of the Lower Castle city seemingly merged into the city’s chain of defensive equipment.

It is also not a coincidence that the attic of the church included a gallery with firing holes, while the facade had towers leading to it. Nevertheless, the church does not give the impression of a gloomy fortress. A masterful brickwork technique provided its architectural structures with the image of lightness and playfulness. Preserved Gothic murals and legends which survived up to the 20th century and describe the untold splendour of liturgical supplies gifted to this church testify that this church was one of the most beautiful temples of Vilnius at the time.

Unfortunately, Vilnius often suffered from fires which significantly damaged the church in 1560 and once again in 1564: all of the interior equipment of the church was destroyed, and its vaults threatened to collapse. Reconstruction works funded by ruler Steponas Batoras, Duke Mikalojus Kristupas Radvila and other wealthy townspeople began only in around 1577 when Leonardas from Sieradz was the custodian. To this day, his contribution to the repairs of this temple is proven by an inscription on the vault above the arch of triumph. Rebuilding took a long time, up to the middle of the 17th century.

The entire monastery complex was once again devastated by the Moscow army during the war in 1655–1661. The church was rebuilt once again in 1676 and consecrated under the double title of St. Francis of Assisi and Bernardino of Siena. This time, the hetman of GDL and Vilnius voivode Mykolas Kazimieras Pacas contributed greatly to the repairs.

Bernardine Church was closed down in 1949. It stood abandoned for several years, but was later given away to Vilnius Academy of Arts and turned into a warehouse.

Only in 1994, the Little Brothers of St. Francis who previously renewed their activities in Lithuania returned to the church once again and initiated the resurrection of Bernardines. Restoration and renovation works are gradually revitalizing the spirit of the church and its art monuments who have long been waiting for a sensitive heart and caring hands.