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The exact date of the construction of the first church is unknown. Some sources indicate that a wooden chapel was built here in 1619. The second church which was also wooden was built in the middle of the 17th century, next to the wooden monastery of Dominicans settled nearby in Gardai. The third wooden church was built in 1750. Constructions of the current church began in 1780 and were finished in 1822. On 7 July of that year, during the Great Feast, the first Holy Mass was celebrated at the Altar of the Holy Cross in Loreto. The church was built from the funds of the faithful.

However, the church was significantly damaged during a major fire in 1896: the fire destroyed several hundred books, archival documents, as well as a book which listed the miracles that were witnessed in Žemaičių Kalvarija. At the beginning of the 20th century, the church was rebuilt after the fire according to the project of architect A. Kosakauskas. The church was not damaged during World War I – only two of its bells were taken away. The church was repaired several times during the interwar period: the most major works were carried out in 1928, when Marians settled in Žemaičių Kalvarija. The interior of the church was repaired in 1939. During World War II, the church was temporarily occupied by the Red Army. The building was repaired several times in Soviet times.

On 6 May 1988, Pope John Paul II promoted the Church of the Visitation of the Blessed Virgin Mary to the rank of a basilica.

Priest Jurgis Kasakauskis (around 1650–1722), the author of the first Lithuanian prayer book, lived in Žemaičių Kalvarija.

The church (small basilica as of 1988) has forms transitioning from the Baroque to the Classicism period, with two neo-Baroque towers, basilica style, a rectangular plan and a three-sided apse. The interior has three naves separated by pillars. It holds a total of 9 altars.

The Church of Žemaičių Kalvarija is one of the most outstanding works of architect Augustinas Kosakauskas (1737–1803). Being a creator of classicism architecture, he could not avoid the influence of the Baroque period when designing the facade of the church and adding Baroque style tower elements. Nevertheless, a system of basic forms is typical in the works of this architect: a clear tendency towards the tranquillity and greatness of classicism and the display of structural elements can be seen next to the Baroque elements.

The church is rectangular with three naves and a three-sided apse. The main facade is flat, with two towers. Ionian pilasters paired on the sides start at the high base fragmented with blades and niches. The paired pilasters also highlight the angles of low towers. A pediment with stylized meander ornaments on the sides and a triangular tympanum decorated with purls is inserted between the towers. Cornices surrounding the church and the towers also have small purls.