An ancient legend tells that in 1364 Lithuanian nobleman named Gostautas, has invited 14 Franciscan monks and gave them a home so they could settle in the country. When Gostautas left, all the monks were killed. Some time later, the nobleman invited other Franciscan monks. New monks he lived in a different place, and the place of the murdered monks he had built a Church, named in honor of the Holy cross.

In 1524, the Church burned down. In 1635, in this place dwelt the priests bonifati. They started their activities with, built a new Church of the Holy cross, founded near the monastery of the same name and opened in the monastery hospital. Later the hospital was converted into a shelter for the mentally ill. Church of Gostautas was reserved for the monastic premises. Psychiatric hospital operated here until 1903, when he was transferred to new buildings built especially for psychiatric hospitals.

In 1737 the Church was again burned. In 1748 the Church was restored, was completely renovated interior, were arranged in six altars, and was installed in the Church pulpit, built in the Baroque style. Also in the Baroque style of the façade and the building of the monastery. Although after this restoration, the exterior of the building appeared and Rococo elements. Inside the temple stands majestically on a spacious stone cruciform arches. Interesting combination of architectural elements of Baroque, Rococo and neo-Rococo.

On the temple grounds is a spring, which is considered miraculous. Legends say that the source appeared suddenly near the statue of the Immaculate Conception. This is the place where he was tortured slain monks, the Franciscans. Say especially beneficial this water on patients suffering from eye diseases.

In the Church there is a miraculous cross, which is mounted above the main altar. Below the cross is the image of the blessed virgin Mary with the infant. Presumably, the picture is painted in the 17th century, but the authentic origin of the painting is unknown. She is also ranked as miraculous creations. The copy of the miraculous painting of the blessed virgin Mary and 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, the Church held a special service for students in Lithuanian schools. During the period when Vilnius was occupied by Poland, not in the Church service was conducted in the Lithuanian language.In 1843 the Order of God was abolished, and the Holy place were only their representation. In 1909 the Church was again repaired. At the end of the First world war, in 1924, Bishop Jurgis Matulaitis was invited by God to return to the monastery of the Holy cross. The monks return to the monastery was very timely. They repaired the Church, erected in six altars. They also organised at the Holy abode of refuge for the elderly and soup kitchen for the needy "Caritas".

At the beginning of the Second world war the brothers from Vilna were withdrawn, in the order of God. In 1947 the monastery sheltered sisters of congregation of the Immaculate Conception of the blessed virgin Mary". However, they dominated here a while. The Soviet authorities closed in 1949, the monastery and the temple. In the buildings of the monastery were located residential apartments.

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

The Vilnius Archdiocese received back their buildings just after the change of regime in 1990. The Church and the monastery buildings were restored, sanctified and sent again to the nuns of the congregation of the sisters of the Immaculate Conception of the blessed virgin Mary".