The complex of the church and monastery has been opened here since 1567. After its reconstruction between 1749 and 1753 (architect January Kristof Glaubic) the church became the only baroque Orthodox sanctuary in Lithuania. The interior was crowned by a wooden iconostas resembling the Catholic altar, under which a crypt was built for the relics of Orthodox saints Anthony, John and Eustatius. In 1853 the relics were relocated to a new reliquary which became their last resting-place until now. 26 June is annually celebrated as a big Orthodox feast — the day of transferral of relics. The last reconstruction of the church was accomplished on the initiative of N. Muravyov. The monastery complex comprises two monasteries: the friary of Holy Spirit (built at the intersection of the 15th and 16th centuries) and the convent of Holy Mary Magdalene (built at the end of the 16th century). It should be noted that both monasteries managed to remain open during the soviet period. Both buildings (reconstructed in the 19th century) have Gothic fragments.
This is the main Orthodox Church in Lithuania. The male and female monasteries next to the church are the only working Orthodox monasteries in Lithuania.
The privilege of constructing the Orthodox Church of the Holy Spirit from stone was granted by the Lithuanian-Polish King, Wladyslaw Vasa. The interior of the church is decorated with stucco mouldings and sculptures, which is not typical of Orthodox churches in other countries. Stucco is a mixture of high-quality plaster and marble, most often white or yellowish. A decorated reliquary in the centre of the Church of the Holy Spirit contains the remains of three Orthodox saints: St. Anthony, St. Eustatius and St. John. The Church of the Holy Spirit in Vilnius is the only Orthodox Church in Lithuania built as a Baroque church in the shape of the Latin cross. By the end of the 16th century, a monastery, a school and a printing shop were situated next to the church. In the 18th century, the Monastery of the Holy Spirit could not avoid the major shocks that shook the city: the Great Northern War, the plague, the Kosciuszko uprising, and later the French invasion. In 1749 the church was badly damaged by fire. It was reconstructed by one of the prominent Baroque architects of Vilnius, Jonas Kristupas Glaubicas (Johan Christoph Glaubitz). The church was again reconstructed in the 19th century.