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On the southeast side, constructions of the Gothic church with a single nave and three-sided apse date back to the end of the 15th century – beginning of the 16th century. The shrine was named the Holy Trinity Church. It was reconstructed after being devastated by fires in 1748 and 1749: a new presbytery and two towers were built, and a new portal was made in place of the Gothic apse. The church belonged to Vilnius University. Astronomer and university’s rector Marcin Odlanicki Poczobutt was one of the parsons of the church. Tsarist government converted the shrine into an Orthodox church in 1821, however it was returned to the Catholics in 1920. The church was abandoned during the Soviet occupation. Part of its facade and portal collapsed in 1968; the old Gothic three-sided apse was restored here in 1971. There is a surviving building nearby, the first floor of which was used as a men’s shelter and the second floor – as a parsonage.

Vilnius Lithuanian Club and Vilnius Lithuanian Student Union were established here after World War I. The building has features of Baroque and Historicism.

The shrine displays the image of Merciful Jesus famous for its graces and visited by many pilgrims. It conveys the visions of Faustyna Kowalska. The painting was made by painter Eugene Kazimierowski in 1934 under the care and by following the instructions of Faustyna. In 2004, the then archbishop metropolitan cardinal Audrys Juozas Bačkis established the Shrine of Divine Mercy of Vilnius within the building which was adapted for the worshiping of the Image of Divine Mercy. Display of the aforesaid image in this shrine caused conflicts within the churchgoer community.

During the Soviet period, the painting disappeared under confusing circumstances and was found during the seventh decade of the 20th century in one of the Belarusian Grodno churches. However, with the efforts of the archbishop of Minsk Tadeusz Kondrusiewicz and the bishop of Grodno Aleksander Kaškievič, the Image of Divine Mercy was secretly brought back to Vilnius and hidden in Vilnius Church of the Holy Spirit in order to preserve it.