The museum has five branches that focus on different aspects of Jewish history and culture. The Tolerance Center's collections include works of sacred, modern, and traditional art along with historical materials; The Green House is a Holocaust exhibit; the Paneriai Memorial is dedicated to the Paneriai (Ponary) Massacre; the Jacques Lipchitz Memorial Museum in Druskininkai exhibits his lithographs; and the former Tarbut Gymnasium displays the history of Lithuanian Jews in the interwar and Nazi period.