For some time Antanas Baranauskas was teaching here, who started lecturing in the Lithuanian language. Many students were active in Lithuanian book smugling. In 1884 students began printing Lithuanian language newspaper "Lietuva", edited by Adomas Dambrauskas-Jakštas. Afraid of persecutions by Tsarist authorities, seminary leaders closed the newspaper. In 1888 secret Lithuanian society was established, that in 1989 was transformed into the St. Casimir Society. In 1892 Maironis was appointed as professor here and this move made a major impact on usage of the Lithuanian language. As he left to St. Petersburg, Adomas Dambrauskas-Jakštas was appointed as the chaplain and continued Maironis' work. In 1909 Maironis was appointed as the rector of the seminary. At the time seminary was completely Lithuanian.
During World War I, the seminary moved to Vašuokėnai estate near Troškūnai as the building in Kaunas was converted to a military hospital. Between 1926 and 1940, 3,078 students graduated from the Seminary. After Lithuania was occupied by the Soviet Union, all other priest seminaries in Lithuania were closed. The number of students was at first limited to 150 but was gradually decreased to 25. Most of the seminary buildings were confiscated, Church of Holy Trinity was turned into a warehouse, library of some 90,000 volumes destroyed, and many priests deported to Siberia. Between 1945 and 1981, 428 priests graduated. After Lithuania declared independence in 1990, the seminary reacquired its former buildings, which were restored before the visit of Pope John Paul II in 1993.