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It is believed that this church which is one of the oldest Gothic churches in Lithuania was built in the second half of the 15th century. In 1503, the Grand Duke of Lithuania Aleksandras (Alexander) assign it to the parish church of Kaunas. A small tower was added to the church in approximately the middle of the 16th century.

The church has a Gothic style, a square plan and a single tower with a narrower and lower square presbytery.

Visitation acts of 1782 state that the church stood abandoned for a long time.

In 1921, it was given away to Marion monks who built a brick monastery in the corner of the churchyard.

Both the church and the monastery were closed down in 1948. The church was turned into a medical equipment warehouse. Administrative offices were established in the Marion monastery, as well as communist parties and executive committees of the Požėla district later on.

Constructions of an additional building for these administrative offices began in 1988 and plans were made to demolish the church, however the public objected to this. Architectural studies of the church began in the summer of 1988. Restoration works of the building began in 1989. Services were held here since 1991.

The first Candle Shrine in Lithuania was built in the vaulted cellar of St. Gertrude Church situated under the presbytery part of the church which along with its outside entrance was built under the church in 1785 – 1794 under the initiative of priest Jurgis Ulazovičius. The Candle Shrine was consecrated on 5 May 2002. At the time, the first 28 candles were lit with the intentions of the benefactors.

The Candle Shrine is part of the Unity of Prayer campaign organized my Marion monks and their helpers around the world, as well as in Lithuania at the miraculous Cross of St. Gertrude Church. Each person can ask for help with prayer both for themselves and others, by giving a certain donation and specifying the purpose for which it was given, or giving no donations at all. A candle is then lit in the Candle Shrine which burns for seven days. During this period, participants of the Unity of Prayer campaign pray to the miraculous Cross for the requested intention. Each person who asks for prayer can also become a participant of the Unity of Prayer campaign and pray for the requested intentions of other people.

The aim is to involve in the Unity of Prayer campaign as many Catholics as possible who visit the Candle Shrine by encouraging them to pray for other members of the society and the universal Church. This way, united in prayer, the faithful can implement the principle of Christian love, perceive oneself and one's neighbour as a member of the Church, and perceive the Church as true unity in Christ. When communicating through prayer, churchgoers feel that here they can help both others and themselves as well. Therefore, the Candle Shrine in the crypt of St. Gertrude Church bears witness to the faith and love of believers, as well as their unity and prayer for one another.