One of McGuinness's middle names, Pacelli, is after Pope Pius XII (Eugenio Pacelli).
McGuinness attended first St. Eugene's Primary School and later the Christian Brothers technical college, leaving school at the age of 15.
McGuinness married Bernadette Canning in 1974; they had four children, two girls and two boys. He was a fan of the Derry and hurling teams and played both sports when he was younger. He grew up just 50 metres from Celtic Park, the home of Derry's Gaelic Athletic Association (GAA). His older brother  played Gaelic football for Derry and is regarded as one of the county's best ever players. He had three medals, as well as and All-Ireland Under 21 Championship medals. He supported Derry City F.C. where his younger brother Paul played for the Candystripes.
McGuinness supported Manchester United from the age of eight. McGuinness also had an interest in cricket – sometimes extending his support to the England cricket team, as well as that of Ireland.