Mudd resided in McLean, Virginia. He was married to the former E. J. Spears of Richmond, Virginia, who died in 2011. They had three sons and a daughter: Daniel, the former CEO of Fortress Investment Group LLC and the former CEO of Fannie Mae; the singer and songwriter Jonathan Mudd; the author Maria Mudd Ruth, and Matthew Mudd. He was survived by 14 grandchildren and two great-grandchildren. Roger, whose last name was Mudd, was a collateral descendant of Samuel Mudd (meaning he descended from another branch within the same extensive family tree), the doctor who was imprisoned for aiding and conspiring with John Wilkes Booth after the assassination of Abraham Lincoln.