The Samogitian Diocese Museum is a museum dedicated to the former Diocese of Samogitia. Established in 1999, the museum is located in the building of the former Varniai Priest Seminary which was relocated to Kaunas after the failed Uprising of 1863. The museum is a branch of the Samogitian Museum Alka based in Telšiai.

Merkelis Giedraitis was Bishop of Samogitia from 1576 to 1609. Educated at Protestant universities in the Duchy of Prussia and Germany, he actively combated the Reformation implementing resolutions of the Council of Trent in Samogitia. Born into the princely Giedraičiai family, he inherited a much neglected diocese that was reduced to only about 20 priests. He became known for his devotion and work to end clerical abuses, strengthen churches and schools, and increase the number of priests. Giedraitis invited the Jesuits to Kražiai where the Kražiai College was established already after his death and the Bernadines to Kretinga where they established the first monastery in Samogitia. He sponsored Mikalojus Daukša, who translated and published Catechism (1595) and Postil (1599) in the Lithuanian language—the first Lithuanian books printed within the Grand Duchy of Lithuania. He also supported Maciej Stryjkowski, author of the first printed history of Lithuania. In recognition of his efforts, Giedraitis is often referred to as the second baptist of Samogitia.