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Wars and unrest in the city did not spare the buildings of Lukiškės Convention. In the second half of the 17th century, they burned several times seeing as all of them were made of wood, therefore constructions of a brick church began in 1690 in place of the old buildings which were not finished until 1727. These constructions were initiated by Vilnius Dominican prior - priest Gnoinskis who collected the necessary funds and prepared the building materials. The church was built in several stages. First, a low nave was built along with two low towers. A presbytery with a semi-circular apse were added later, while the height of the nave was increased. A pediment was built in 1718 by J. Daukševičius. However, works were not finished yet. In 1727–1737, third and fourth tower tiers were built according to the project of architect Abrahamas Antuanas Genu. Three bells with the inscriptions of years– 1711, 1738 and 1739 were hanged in the towers. The Chapel of St. Hyacinth was built under the southern tower which was known for its altar of artistic forms and compositions painted on cross vaults depicting the life of St. Hyacinth.
The interior of the church was also gradually built. In 1743–1744, the walls of the interior were decorated and an organ choir tribune was built. Later, organ master Gerardas Celė made an organ positive. An old, miraculous image of Our Lady of Mercy painted on wood was added to the high altar. It was brought from Russia in 1649. At first, the painting was kept in the home chapel of Dembliai Manor, near Sejny along with another image of the Mother of God. Both paintings were transferred to Sejny Dominican Church. In 1684, the prior of the aforementioned convention gifted the painting of Our Lady of Mercy covered with silver linings to the Dominicans of Lukiškės, while the second painting was given to the Monastery of St. Michael the Archangel in Trakai. In 1894, the miraculous painting in the Church of Apostles St. James and St. Philip was decorated with various precious stones from the funds of priest J. Kurčevskis. The painting disappeared in 1948, when the church was closed down and converted into a fruit-vegetable warehouse, and later an opera and ballet theatre warehouse. Only in 1998, it became evident that the painting was safely stored for half a century in Vilnius St. Raphael Church from which the sacred item was recovered by the Dominicans at the Church of Apostles St. James and St. Philip.
In 1713–1739, brick monastery houses were added to the church. They had two floors, an L shaped plan which was turned into a Z shape after one more wing was added to the ensemble at the end of the 18th century. The monastery had 10 cells situated on one side of the corridor. There was a school near the monastery where lessons were held by the Dominican parents themselves.
Lukiškės Parish of St. Jacob managed the Chapel of St. Hyacinth in Basanavičiaus street. There is a record that testifies that this monument was built in 1403 by Dominican St. Hyacinth who was an apostle in Lithuania in the middle of the 13th century. The decor of the vaults of the Chapel of St. Hyacinth was made in his honour. Lukiškės Dominicans renewed the monument in 1762, built a wooden sculpture portraying St. Hyacinth and added a marble plaque with an inscription. The deteriorated chapel was rebuilt in 1843 with the funds of cultural figure Kazimieras Vilčinskis and other residents of Vilnius. In 1901, it was restored: a new sculpture of St. Hyacinth was erected, while the old one was transferred to the Church of Apostles St. James and St. Philip and placed in the Chapel of St. Hyacinth.
When the church was returned to the faithful in 1992, the restored Dominicans settled in the monastery after a year. The headquarters of the general vicarage was established here joining together Dominicans in Belarus, Estonia, Latvia and Lithuania. Recently, the reconstructed side altars were decorated with newly created images of saints worshiped by the Dominicans. It should be noted that parents communicate with the public in various ways. By cooperating with the Academy of Music, they organize concerts of classical and church music in the Church of Apostles St. James and St. Philip