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McDonald has written extensively about the Troubles and related issues. He was born in the Irish nationalist Markets area of Belfast and attended St. Malachy's College. McDonald was formerly involved in Workers' Party of Ireland, a left-wing party that emerged from Sinn Féin in the early 1970s and was associated with the Official IRA. He travelled to the German Democratic Republic (East Germany) with the youth wing of SFWP in the early 1980s.
Much of his writing concerns paramilitary groups in Northern Ireland, like the Ulster Defence Association (UDA) and Irish National Liberation Army (INLA). He has written a book on the INLA, INLA - Deadly Divisions, which he co-authored with the now deceased Jack Holland. The book was first published in 1994 and has since been re-printed and updated.
More recently, McDonald has written on Ulster loyalist paramilitary groups and has co-authored books on the Ulster Volunteer Force (UVF) and UDA with Jim Cusack. He also wrote a biography of Ulster Unionist Party (UUP) leader David Trimble, a personal biography "Colours: Ireland - From Bombs to Boom"  and in 2017, "Martin McGuinness: A Life Remembered". He was, for a period, a security correspondent for the BBC in Belfast. During the 1990s he was a staff reporter at Belfast newspaper The Irish News, where he edited the youth pages.
McDonald is a supporter of Cliftonville and Everton. He has two daughters and a son from marriage. He also spent twelve years with author June Caldwell  living some of that time in Dublin where he taught journalism and feature writing at the Dublin Business School and the Irish Writers Centre. 
Henry McDonald is Ireland correspondent for the Guardian and Observer.