The Samogitian Diocese Museum was established in 1999 in a late Baroque building, the residence of the former Samogitian Theological Seminary. It was built in 1770-1771 by the concern and expense of the Bishop Jonas Dominykas Lopacinskis. Over the centuries the owners and the purpose of the residence changed several times. The uncared-for building was heavily damaged during the Soviet times. After the restoration of Lithuanian independence, the reconstruction of the residence began. Over 1991-1995 the bell tower was rebuilt, as well as the typical late Baroque roof construction. The reconstruction works were not yet completed, thus the Museum operates only in the southern wing, as well as other renewed premises of the residence.

The purpose of our museum is to collect, preserve and present the artistic, historical and memorial heritage of the Samogitian Diocese and Telšiai Diocese, as well as other museum valuables to the public and to continue the Christian tradition of the region and the country. The museum also provides cultural, educational and informational services, which help to maintain and strengthen the historical, cultural and religious identity of the citizens of Lithuania.

From 15th to the beginning of the 20th century there were two dioceses in Lithuania - Vilnius Diocese and Samogitian Diocese. Samogitian Diocese was established in 1417 and for a couple of centuries used to be called Medininkai Diocese. Varniai was its centre for almost 450 years. The city's role in the religious, cultural and political life of Lithuania was special and has left a distinctive mark on the country's culture and history.

In the summer of 1417, Vytautas, the Grand Duke of Lithuania, together with bishops from Vilnius and Lvovo, visited Samogitia and baptised thousands of Samogitians. Vytautas himself chose Varniai as the place for the centre of the Samogitian Diocese. The Medininkai (or Samogitian) Diocese was established and the cathedral church was consecrated at the end of 1417. The processes specific to the European culture taking place here, made Varniai an exceptional place already in the 15th century. Varniai held the position of a cultural centre for a long time, although the town itself did not grow into a larger urban centre.

In 1623 the first Theological Seminary was opened in Varniai. After some time it was transferred to Kražiai, but after a century returned back to Varniai, where at first it operated in a wooden building and was later moved to the newly built residence, which currently hosts the museum. Thus Varniai became the actual centre of the Samogitian Diocese with an operating seminary, according to the Bishop Motiejus Valančius - the "seedbed" of priesthood. During the second half of the 16th century, Varniai gathered the most prominent Lithuanian clergy: the Bishop Merkelis Giedraitis, the preacher Petras Roizijus, the cannons - the translator Mikalojus Daukša and the historian Maciej Stryjkowski. The bishops, who worked here over the later centuries - Antanas Tiškevičius, Jonas Dominykas Lopacinskis, Juozapas Arnulfas Giedraitis and, of course, Motiejus Kazimieras Valančius were also known for their various contributions to faith, moral education and construction works.

In the 19th century, when the Russian czar closed the University of Vilnius, Varniai Theological Seminary, along with Vilnius’ Medical School, were the only schools of higher education in Lithuania. For this period they became the most important centres of Lithuanian culture.

Varniai Theological Seminary was rightfully considered as the cradle of Lithuanian national movement. Many of its students and workers later became famous writers, cultural or church activists who contributed to Lithuania’s national independence movement. Among them almost all the most prominent representatives of the Lithuanian clergy of the time - Antanas Strazdas, Jurgis Pabrėža, the already mentioned Motiejus Valančius, Antanas Baranauskas, Juozapas Silvestras Dovydaitis, Antanas Vienažindys and many other enlightened persons.

Varniai Theological Seminary operated until 1864. When the uprising of the 1863 was defeated, the administration of the czarist government forcibly moved the curia of the Samogitian Diocese and the Theological Seminary to Kaunas. Then the building of Varniai Seminary was transferred to the Russian National Defence Army - the regiment of Don Cossacks. During the period of the independent Lithuania, the buildings of the former seminary housed the Disciplinary Battalion of the Lithuanian Army as well as the regiment of the Duke Vaidotas. During 1927-1931 it housed a concentration camp, later - Varniai Secondary School. When the buildings were transferred to Varniai Vocational Technical School, they were reorganized into dormitories and warehouses. In 1999 by the decision of the Government of the Republic of Lithuania the partially reconstructed residence was given to the Samogitian Diocese Museum.

The author of the sketches of the architecture of the building is the most famous late Baroque architect in the Grand Duchy of Lithuania of the 18th century Johann Christoph Glaubitz. His works in Lithuania include the reconstruction of the St. Johns' Church in Vilnius and the creation of its facade, which, harmonious as a symphony, has survived to our days, as well as the Basilian Gate and the most graceful towers of the Missionary Church. The famous architect was invited to Varniai by the Samogitian Bishop Antanas Tiškevičius. Johann Christoph Glaubitz died early, before he finished the works started in Varniai. Then the Bishop Tiškevičius' successor Jonas Dominykas Lopacinskis invited another architect to lead the construction of the seminary - Johann Wilhelm Frezer.

At the enter of the the seminary building, on the ceiling visitors can see the exposed bricks. They demonstrate the meeting of the buildings of two periods - the bell tower and the later u-shaped wing of the seminary building. The bell tower was constructed circa mid. 18th century, while the seminary was bricked during the 8th decade of the 18th century. Thus, these openings show how two asynchronous buildings merge into a single residence. Its external composition, designed by the architect Glaubitz, reminds us of the architectural type of the Northern European Renaissance town halls. Unfortunately, quite soon - in 1785 - this glorious building was devastated by fire. The bell tower, which was unsuccessfully built in such a long time, burned down and the bells hanging there melted from the heat. The building was left without a tower, only with a simple low span roof for as much as two centuries. Reconstruction works began only after 1990.