The Sejny Seminary was established by bishop Mikołaj Jan Manugiewicz to address shortages of Lithuanian-speaking priests.
[2] A large portion of the students were sons of Lithuanian peasants from Suvalkija.
In 1915, during World War I, the seminary was evacuated into Russia (first Mogilev, then Saint Petersburg).
[2] In 1919 the seminary returned to Sejny, but the town was at the center of the Polish–Lithuanian War.
After the Polish seizure of Sejny after an uprising done by the Polish Military Organisation in August 1919, the Lithuanian students and faculty were expelled into Lithuania, where the seminary continued in Zypliai and Gižai.