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The word of God was already being spread in Kaunas in 1550 according to the unaltered Augsburg Confession of Faith. A parish was established in 1558 and was managed by priest Zommer who served here until 1570. The second priest of the parish was Bampf, followed by priest Oderborn (or Oldenborn). It is unclear for how long they have served here. What is known is that in 1577 services were held in the first small Evangelical Lutheran church at the Town Hall Square near the current house of Maironis. Priest Pannachius served here between 1588 and 1591. Later on, the church had the following priests: Pase, Vegner, Movius, Sperber, Eingler, Möler, Lange Bandreus, and Rüdel. The church building burned down during a large fire.
A bell tower was built in 1862 (architect J. Woller). However, the church was closed down in 1953, because it supposedly did not have enough churchgoers. During the Soviet era, the church was given away to Vilnius University Kaunas Faculty and converted into an auditorium. The church that was closed down during the Soviet period was restored in 1989 and is currently attended by both the Evangelical Lutherans and the Evangelical Reformed.