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The church – spiritual centre of the town was similar in size and importance to the palace of Trakai Island Castle. The church is exceptional not only in its size, but also in its unique history – it has never been closed down, transferred to another confession or used for other purposes. Today, Trakai Church is a unique monument of faith and Lithuanian cultural history protecting the multi-layered, 600 year old Church and art heritage. 

Trakai Parish Church was established under a foundation privilege on 24 May 1409 by the Grand Duke of Lithuania Vytautas. It was then given the title of the Visitation of the Blessed Virgin Mary and St. John the Evangelist. Bezděz parish was assigned to support the three priests of the church, and a wage was paid to the cleric or school manager. A foundation privilege is an act of will and power. It grants resources for the construction and equipment of the church. It is unknown when the constructions of the church were completed or when it was consecrated. The pastor of the church was first mention only in a document from 1479. Therefore, the building was already consecrated at the time and church services were being held, however the date of consecration remains unknown. After evaluating the historical circumstances, it is likely that constructions of the church were carried out by the same persons who built Trakai Island Castle. Materials collected from the constructions of the castle may have also been used. Thus, it is likely that the church was built at the end of the second decade – beginning of the third decade of the 15th century. This red bricked Gothic building stood until the beginning of the 17th century, when an entryway was added in the light of changes in the liturgy. At the time, the church became famous for its miraculous image of the Mother of God and the clemency received from it by praying people. Historical sources state that the number of praying people was growing, and the church inventory lists gifts for the graces granted by the Mother of God. The number of buried people in crypts was increasing.

During the war with Moscow in 1655–1661, the church was robbed and damaged. It was reconstructed in the style of the Baroque period after the war. In 1700, under the initiative and with the funds of General of the Army of the GDL Matas Römeris, Römeriai family chapel was built at the southern wall of the presbytery.

The history of the church is closely related to Lithuanian statehood and devotion to the Blessed Virgin Mary. During the times of the Grand Duchy of Lithuania, Trakai Church was funded by the rulers of the state. In 1803, the church and its property were transferred to be managed by Vilnius University. Devotion to the Mother of God of Trakai decreased at the time. However, in the 19th century, Trakai was once again famous for its miraculous image of the Blessed Virgin Mary, and the church became one of the most important shrines of Virgin Mary in Lithuania. The church building was damaged in the 20th century during both wars, and was also poorly taken care of during the Soviet period. However, educated Catholics of the Soviet era, particularly those from Vilnius, often came to Trakai in order to receive sacraments in the shrine which, based on the memory of the history of the state, was mostly similar to Vilnius Cathedral which was closed down by the Soviets.

Trakai Church is currently being restored. It is likely that a thorough restoration will reveal many unknown historical facts.

The massive masonry and the image of the church in Trakai town panorama carved in around 1600 by Tomas Makovskis hint how the Gothic church building may have once looked. The church is displayed as a hall style building with a double-sided roof and a significantly lower apse. The churchyard is shown with a separately standing bell tower. The current church plan and brick studies show that the old church had three structural parts and three naves – with the side ones being much narrower than the middle one. The wide central nave extended to an asymmetric three-sided apse. The arch was most likely supported by massive presbytery abutments, and the wooden ceiling above the naves was held by four profiled columns. The main entrance was located in the western facade of the building, while the side entrance – on the northern wall. There may also have been a door leading to the sacristy.