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In 1463, a new wooden Cathedral was built by Medininkai bishop Jurgis Vilnietis (1453–1464) with the help of the Grand Duke of Lithuania Casimir, and was given the title of St. Peter and St. Paul. Varniai Cathedral was built on another side of the river, in Medininkai, where the palace of the former Varniai priest seminary now stands. Vilnius voivode Mikalojus Radvila began building a brick church in 1519, however he was not able to complete its constructions. In around 1555, a wooden church was built on top of the brick foundation, but it was destroyed during a fire that broke out in the town in 1680. The churches burned down here and were rebuilt at least three times.

The current brick church was built in another location, in 1681–1691. A wooden priest seminary house was built in 1739–1740, and a brick one was built in 1771. The priest seminary was relocated here from Kražiai in 1740.

The cathedral was damaged during a fire in 1817. Bishop Juozapas Arnulfas Giedraitis repaired it for 15 000 silver roubles. In 1821, a church organ built by local master Juozapas Vaiciulevičius was added to the cathedral. The organ was remade by Pranciškus Sideravičius in 1871. In 1864, the cathedral became the New Varniai parish church to which all the Catholics living on the left bank of Varnelė were assigned. A fire broke out in the town in 1864 which destroyed the diocesan archive, however, some of the files were saved. In 1867, roof tiles of the church were demolished by a storm and its exterior plaster crumbled.

Varniai Church of the Apostles St. Peter and St. Paul, the former Cathedral, is an interesting architectural monument. The building itself is massive with a modest exterior and a rich interior. The church has Baroque features, basilica style, a cross plan, and two towers. Its longitudinal axis is oriented to the west and east. The interior of the church has three naves. The central nave is higher and wider than the side naves and covered with a cylindrical vault. It is separated from the side naves with massive pillars. The central nave is extended by a presbytery ending with a three-sided apse supported by abutments. Two-story sacristies can be found on both sides of the presbytery. The side chapels are completed with modest Baroque pediments. Slightly protruding, square towers with three-tiers, rather stocky proportions, and curvy roofs can be found in the main facade on the western side. An entryway is built on the south side.