Originally, Slabodka boasted the famous Knesses Yisrael yeshiva, founded by Rabbi Nosson Tzvi Finkel in 1882. However, in 1897, controversy broke out in the yeshiva, as many of the students were opposed to the yeshiva strong focus on mussar (Jewish ethics), as opposed to only studying Talmud. The yeshiva therefore split into two, with the one against mussar going under the name Knesses Beis Yitzchok (named for the previous rabbi of Kaunas, Rabbi Yitzchak Elchanan Spektor). The rav of Slabodka, Rabbi Moshe Danishevsky, served as rosh yeshiva. Rabbi Moshe Mordechai Epstein, the rosh yeshiva of Knesses Yisrael, served alongside Rabbi Danishevsky in the town's beis din (Torah court). Despite the friction between the two yeshivos at the time of their division, the cooperation between the two rosh yeshivas thawed the ice. Rabbi Chaim Rabinowitz also served as rosh yeshiva. However, a controversy between pro- and anti-Zionists broke out in the yeshiva, and Rabbi Rabinowitz left the yeshiva. Rabbi Baruch Ber Leibowitz, a student of Rabbi Chaim Soloveitchik and formerly a rosh yeshiva in Halusk, was appointed as rosh yeshiva.
