He had eight children by his first wife, Chaya Ruda Czarna, daughter of Noach Czarny, a prominent Gerrer Hasid in Biala. His eldest son, Rabbi Meir Alter, who was a Torah scholar and businessman, perished in Treblinka during the Holocaust with his children and grandchildren. His second son, Rabbi Yitzchak Alter, died in 5695 (1934) in Poland. In 1922, his wife Chaya Ruda died. Some time later he married his niece, Feyge Mintshe Biderman, who bore him his youngest child, Pinchas Menachem Alter, in 1926.