Kovno, from where the members of the Kovner Verein emigrated to the United States, had Jewish participation in the trade between Kaunas and Danzig in the 16th century. Their competition aroused opposition from the Christian merchants, and through their influence Jews were prohibited from Kaunas on numerous occasions. However, the ban was not strictly enforced, and gradually a small group of Jews settled in Kaunas. The ban was renewed in 1682, and Jews were not permitted to settle in Kaunas and engage in trade until the 18th century when they were permitted to reside in two streets. In 1753 they were expelled from land belonging to the municipality. The Jews were again expelled in 1761, when there were anti-Jewish riots. They found refuge in the suburb of Slobodka (Vilijampole) on the other side of the River Viliya, where a Jewish settlement had existed long before that of Kaunas. In 1782 the expelled Jews were permitted to return to Kaunas. After the partition of Poland in 1795 Kaunas became part of Russia. In 1797 the Christians in Kaunas again demanded the expulsion of the Jews, but the authorities in 1798 ordered that they should be left alone, and not be prevented from engaging in commerce and crafts. Restrictions on Jewish settlement there were again introduced in 1845 but abolished in 1858. The Jewish population increased as the town expanded. There were 2,013 Jews living in Kovno (Kaunas) and Slobodka in 1847; 16,540 in 1864; 25,441 in 1897 (30% of the total population); and 32,628 in 1908 (40%).

From the second half of the 19th century, Kovno became a center of Jewish cultural activity in Lithuania. Prominent there were R. Isaac Elhanan Spektor (the "Kovner Rav,"; officiated 1864–96), Abraham Mapu, one of the first modern Hebrew writers, and the literary critic Ba'al Makhshoves (Israel Isidor Elyashev). The yeshivot of Slobodka became celebrated, in particular the Or Hayyim yeshivah, founded by R. Zevi Levitan about 1863, which attracted students from other countries. It was headed by noted scholars. Nathan Zevi Finkel introduced musar ideals there; from 1881 it was known as the Slobodka yeshivah. Subsequently there was opposition among the students to the musar method, and in 1897 the yeshivah was divided into two: the followers of musar established the Keneset Israel yeshivah, named after Israel Lipkin (Salanter), while its opponents founded the Keneset Bet Yizhak yeshivah, named after Isaac Elhanan Spektor. In May 1869 a conference was convened at Kovno to help Jewish refugees from northwestern Russia where the failure of the crops had led to famine and an outbreak of typhus. Another was held in November 1909 to work out a proposal for a law to establish Jewish community councils in Russia. The Kovno community maintained numerous hadarim, schools, and libraries. It returned Jewish deputies to the first and second Duma (L. Bramson and Sh. Abramson). The Jews in Kovno underwent many vicissitudes during World War I. In May 1915 an edict was issued by the czarist government expelling the Jews from the entire province. When later the city was occupied by the Germans, about 9,000 Jews returned, and communal life was revived with the help of Jews in Germany. Many who had been expelled to the Russian interior returned after the 1917 Revolution. Most of the Jews of Kovno were murdered during the Holocaust. Most of the survivors from Kaunas eventually settled in Israel. Jews settled there from other places, however. The Jewish population numbered 4,792 (2.24% of the total) in 1959. There was a synagogue. In 1961 a Jewish amateur theater troupe (Yidisher Selbsttetigkeyt Kolektiv), consisting of a drama group, choir, orchestra, and dance group, was organized in Kaunas, holding public performances from time to time. In 1963 the Jewish cemetery was plowed up and Jews were ordered to bury their dead in the general cemetery. However, at their request, they were permitted a separate Jewish section. Several incidents in which Jews were beaten up in the streets were reported in 1968.