An ancient legend tells that in 1364 Lithuanian nobleman named Goshtautas invited to 14 Franciscan friars and gave them home so that they could settle in the country. When Goshtautasa left, all the monks were killed. Some time later, the nobleman Invite Franciscan monks. New monks he settled in another place, and the place of the murdered monks, he built a church, named in honor of the Holy Cross.

In 1524 the church burned down. In 1635 in this place settled priests Bonifratrzy. They started their work with, built a new church of the Holy Cross, founded near the monastery of the same name and opened at the monastery hospital. Later, the hospital turned into a shelter for the mentally ill. Goshtautasa Catholic church was allotted by the monastery premises. The psychiatric hospital operated here until 1903, when it was moved to the new building constructed specifically for the psychiatric hospital.

In 1737 a church was burned again. In 1748 the church was renovated, the interior has been completely repaired, six altars were built and installed Kost'ol'na Department was built in the Baroque style. Just decorated Baroque facade and the building of the monastery. Although after the restoration of the exterior of the building and there were elements of Rococo. Inside the temple stands majestically over the spacious rooms stone cruciform arches. Interesting combination of architectural elements of baroque, rococo and neo-rococo.

At the temple there is a source, which is considered miraculous. Legends say that the source appeared suddenly near the statue of the Immaculate Conception. This is the place where the monks were tortured slain Franciscans. They say that is especially beneficial water of this source on patients suffering from eye diseases.

In the church there is also a miraculous cross, which is mounted above the main altar. Below the cross is an image of the Blessed Virgin Mary with Child. Presumably, the picture painted in the 17th century, but for sure the origin of the painting is unknown. It is also ranked among the miraculous creations. A copy of the miraculous painting of the Blessed Virgin Mary with Child, in the form of frescoes can be seen on the main facade of the church. It is under an arched pediment, built in 1737 between the two side towers of the church.

Between 1914 and 1924 in the church held a special service for students of Lithuanian schools. At a time when Vilnius was occupied by Poland, were not conducted in the temple service in the Lithuanian yazyke.V Bonifratr 1843 Order was abolished, and in place of the monastery remained only their representation. In 1909 the church was again repaired. At the end of the First World War, in 1924, Bishop Jurgis Matulaitis Bonifratr invited to return to the monastery of the Holy Cross. Return of the monks in the monastery was very timely. They repaired the church, erecting six altars there. They also staged at the monastery a shelter for the elderly and the soup kitchen for the needy "Caritas".

At the beginning of World War II, the brothers from Vilna were withdrawn Bonifratrzy Order. In 1947, the monastery sheltered by the sisters of the congregation "of the Immaculate Conception of the Blessed Virgin Mary." However, they are dominated by short-lived. Soviet authorities closed in 1949 and the monastery and church. The buildings of the monastery were located residential apartments.

In 1976, the temple was restored and arranged in it the Vilnius Philharmonic Concert Hall, the so-called "Small Hall of the Baroque." There were concerts of organ music.

Vilnius Archbishopric got back to their houses only after the change of regime in 1990. The temple and monastery buildings were restored and transferred to the newly consecrated nuns of the Congregation Sisters "Immaculate Conception of the Blessed Virgin Mary."