The Church was built by the Jesuits: work began on it in 1604, just two years after St Casimir had been canonised. It was dedicated to the memory of Saint Prince Casimir. The legend has it that as many as 700 people rolled the cornerstone from Antakalnis to the centre of the city. Today the stone can be still seen in the wall of the façade.
The Church was completed in about 1616, the interior was finished in 1618. The Church of St Casimir is one of the first Baroque churches in Vilnius. It is thought that Povilas Bokšta designed the church and Jonas Frankevičius performed works on it. It is important to note that in the 18th century, under supervision of Tomas Žebrauskas, the dome of several tiers with a tall lantern and a crown on its top, was built. This is the only dome of such a size in all former lands of the Grand Duchy of Lithuania. Later the Church was taken over by the Russian Orthodox Church, made into a cathedral, and rededicated to St Michael. The famous Russian writer Fiodor Dostojevski prayed in this Orthodox Church. In the first half of the 20th century the Church was returned to the Jesuits but during the Second World War it suffered greatly, and was closed. In 1961 it opened as a museum about atheism, and continued to be used as such until 1988. In 1989 the Church was returned to the Catholic church.