Outside Regimentation of the Catholic Church in Lithuania began after the country’s absorption by the Russian empire (1795) and continued until the beginning of the 20th century. In 1798 the dioceses of Vilnius and Samogitia were annexed to the newly created archdiocese of Mohilev, which, embracing all of Asia and three quarters of European Russia, was the world’s largest. Meanwhile, a new diocese of Vygriai (Wigry), renamed that of Seinai (Sejny) in 1818, was established in southern Lithuania and joined to the archdiocese of Warsaw. Both of the archdioceses were formed in cooperation with the Vatican, but subsequently Czarist Russia embarked on a course contrary to the canons of the Church. Thus, a non-canonically fashioned Roman Catholic Collegium was active in St. Petersburg from 1801 on. Its chairman was the metropolitan of Mohilev, with two assistants appointed by the Czar, and six members delegated by the dioceses. Through this institution the Russian government sought to bind the local Church to a collegiate principle of administration and to weaken the authority of the Pope. To advance this objective even further, each diocese was provided with a consistory (1842) whose secretary was appointed by the government; this official was empowered to choose the other members and to veto any unacceptable decisions. A concordat drawn up between Russia and the Vatican (1847) to restore the previous system was not decreed as law by the Czar and was, in fact, frequently violated.

In contravention of this concordat, the Czar themselves appointed persons subservient to them as bishops, whom Rome was eventually forced to recognize. In this way Vilnius lacked a duly appointed bishop for several lengthy periods totaling more than 70 years, being governed only by temporary administrators. The Samogitian diocese was somewhat better off in this respect. Without government consent, bishops were not allowed to enter into correspondence with the Pope, to leave the boundaries of their diocese, to establish new parishes, or to appoint parish priests and seminary rectors and professors. These and other restrictions on the activities of bishops resulted in ecclesiastical affairs coming under Russian government control. This control became especially repressive following the insurrections of 1831 and 1863. Landed and capital holdings of the Church were confiscated in 1841 – 42. Monasteries and churches were closed. Out of a total of 350 monasteries operating in ethnographic Lithuania at the beginning of the 19th century, only 6 were left open, but even these were barred from accepting new candidates. During the years 1863 – 66, 32 churches and 52 chapels were closed. Church buildings were transformed into barracks, military hospitals, or Russian schools. Without permission from the government it was not allowed to repair old or construct new churches and parish facilities. Public church processions, group pilgrimages to shrines, ceremonial reception of bishops, and erection of wayside crosses were outlawed. Beginning in 1832, sermons had to be submitted for censorship prior to delivery; later they were restricted to texts appearing in certain government–approved publications. Even parish priests were forbidden to visit other parishes without police permission. During 1863–70 not a single new cleric was allowed to enroll in a theological seminary. Schools of this type were operating in Vilnius, Kaunas, and Seinai, while a single Theological Academy in St. Petersburg (moved from Vilnius in 1842) served all of imperial Russia. All parish schools were shut down in 1864. Public school pupils were compelled to pray in Russian and to attend Orthodox services. In order to force Lithuanian Catholics to read religious texts in the Cyrillic alphabet, the printing of anything in Latin characters was prohibited.

The purpose of these and other repressive measures was to Russify and de–Catholicize Lithuanians. In consequence, during 1863–65 alone, 100 Orthodox churches were newly built or reconstructed. But the government’s policies caused Lithuanians to rally to the defense of their faith and alphabet. Motiejus Valančius, bishop of Samogitia from 1850 – 75, inspired and for some time led an anti – Russian resistance effort which contributed decisively towards a change in those policies. As a result, the Russians abandoned their campaign against roadside crosses (1878), revoked their prohibition on the construction of new churches as well as their order compelling Russian prayers in schools (1897), and finally repealed their Press Ban (1904). After the partially successful revolt of 1905 the Catholic Church substantially re-acquired its autonomy, as did Lithuania itself at the end of World War I (1918).