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The Samogitian Diocese Museum is now established here which preserves the art, history, memorial heritage and other museum treasures of the Samogitian Diocese (until 1926) and Telšiai Diocese (from 1926).


It is believed that the hill on which the palace was built was once a place of pagan cult rites. There was also a large cemetery here in the 13th – 17th century. The first two Medininkai diocese cathedrals were built here. After they were destroyed by fire, in around 1740, bishop Antanas Domininkas Tiškevičius began building a brick bell tower here. In 1770, bishop Jonas Dominykas Lopacinskis built a palace near the almost finished bell tower and established the Varniai (Samogitian) Priest Seminary in it. The building was used as a seminary until 1864, when the centre of the Samogitian Diocese, the priest seminary and bishop Motiejus Valančius were forcibly transferred from Varniai to Kaunas.


In 1864, the building was occupied by the Don Cossack Regiment of the Russian Imperial Army which stayed in Varniai until 1905. The palace underwent massive repairs in order to convert it into soldier barracks. After the restoration of independence of the Republic of Lithuania, the Lithuanian Army Discipline Regiment and the 8th Infantry Regiment of the Kaunas Duke Vaidotas were established in the former priest seminary complex.


After the building was repaired, it was used as Varniai secondary school in 1947–1961. In 1964, the building was transferred to Varniai Vocational Technical School which converted it into dormitories and warehouses later on.


In 1984–1990, historical, archaeological, architectural, engineering and geological studies were carried out in the Varniai Priest Seminary building. In 1991–1995, the bell tower of the building and its original roof structure of the late Baroque period were rebuilt. In 1999, under the resolution of the Government of the Republic of Lithuania, the palace was transferred to the Samogitian Diocese Museum. During the same year, a monument for Samogitian bishop Merkelis Giedraitis and canon Mikalojus Daukša made by sculptor Arūnas Sakalauskas was placed near the palace in 1999 under the initiative of the Samogitian Cultural Society. Constructions of the monument were continued both by the Government of the Republic of Lithuania and by Mykolas Giedraitis, a professor at Oxford University who was also member of the well-known family of Samogitian bishops (Giedraitis family).