McCarthy and his wife had five children, Christopher Joseph McCarthy (April 30, 1946 - April 30, 1946), Eleanor McCarthy Howell (born October 30, 1947), Mary Abigail McCarthy (April 29, 1949 - July 28, 1990), Michael Benet McCarthy (born April 5, 1952) and Margaret Alice McCarthy (born July 17, 1956).
In 1969, McCarthy left his wife, Abigail, after 24 years of marriage, but the two never divorced.