In the 17th century Jesuits prayed at various Kaunas churches (mostly St. Nicolas Benedictine and parish churches) and temporary chapels. The construction of Kaunas St. Francis Xavier church started in 1666 and continued until the 18th century. The construction work was disrupted by the Russian occupation of the middle of the 17th century, when the monastery was destroyed, the war of the beginning of the 18th century and the plague which followed this. Finally, in 1720 the main construction work was finished, and the main St. Francis Xavier church altar was consecrated in 1722. The church construction and interior were finished in 1762.

Asta Prikockienė