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Bernardine Sisters settled in Kaunas in the middle of the 16th century. They acquired a wooden monastery which was exchanged for a brick one in 1595. Kaunas marshal (who later became the voivode of Minsk) Aleksandras Masalskis bought new holdings and gifted them to the Bernardine Sisters. There was a fire in the city in 1624 which destroyed the aforesaid buildings. They were not rebuilt and the entire area was re-planned.

A new brick church and monastery were built in 1625–1634 (funded by A. Masalskis). The wall of the former house is merged into the lower part of the western wall of the church, while the end of the former house with an arched entrance is merged into the central monastery palace. The area of the monastery is surrounded by a high brick wall. The ends of three houses that once stood here are merged into it. The church and all of its archive burned down during a fire in 1668. The rebuilt church was consecrated in 1703. In the 18th century, the height of its bell tower was increased.

A brick wall was built in 1782 separating the farmyard (most of the fence was demolished in 1938). Dabravolė and Zapyškis farmsteads of the monastery became the property of Prussia in 1795. In place of these farmsteads, the monastery received Remizavas farmstead of the Ašmena (Ashmyany) county.

The monastery was closed in 1864. Headquarters of the Samogitian Diocese and the priest seminary were transferred from Varniai to the western part of the monastery. The eastern part with the church became the property of Kaunas parish (library of the seminary was established on the first floor of the central building only until 1935).

The church was repaired in 1899. The interior of the church, its roof and organ were damaged during World War I. On 26 September 1926, there was a clash between Lithuanian and Polish believers in the church. Two more floors were added to the western wings of the monastery in 1929 according to the project of engineer Vaclovas Michnevičius (their western part was demolished during World War II; only one four-storey wing remains).

In the 17th century, a tower was built (next to the former cemetery) on the south side near the church. A 3-storey administrative building of the priest seminary was added between the tower and the Holy Trinity Church according to the 1933 project of engineer Karolis Reisonas.

During the independence years, this was a parish church, however it was given away to the Salesians in 1938. The interior of the church was rebuilt in 1939 according to the project of architect prof. Mykolas Songaila. In 1942–1944, around 200 Jews were saved by the parson of the parish Salesian Bronius Paukštys (1897–1966) with the help of other priests.

In 1940, the parish had 5643 parishioners. After World War II, it was used for seminary purposes for some time.

The church was closed in 1962, its interior was destroyed and it was given away to a book depot warehouse. Reconstruction and renovation works of the church and the former monastery began in 1969 according to the projects of architects Birutė Kugevičienė and Liuda Perevičienė. In 1978, the sanctuary was transferred to the Priest Seminary. The seminary used its own funds to restore the Church of the Holy Trinity and build a modern interior – modern altar, chandeliers, church organ and stained glass. On 17 February 1982, the first concelebrated Mass was held by bishop Liudvikas Povilonis in the church whose repairs were not yet finished.

The church is of the late Renaissance period (with Gothic features), with a hall style, outbuildings and a tower on the side. Its high roof and apse have small towers. The interior has three naves separated by pillars. The vaults are stellar and cross-shaped. There are a total of 9 altars. Next to the church, there is a brick 3-storey priest seminary building and a brick 2-storey central palace of the former monastery joined together with an interjacent 2-storey wing. The area of the ensemble is surrounded by a high brick wall.