• Nothing Abides (2015) Daniel Pipes, New Brunswick and London: Transaction Publishers
  • Miniatures: Views of Islamic and Middle Eastern Politics (2003), Transaction Publishers, ISBN 0-7658-0215-5
  • Militant Islam Reaches America (2002), W.W. Norton & Company; paperback (2003) ISBN 0-393-32531-8
  • with Abdelnour, Z. (2000), Ending Syria's Occupation of Lebanon: The U.S. Role Middle East Forum, ISBN 0-9701484-0-2
  • The Long Shadow: Culture and Politics in the Middle East (1999), Transaction Publishers, ISBN 0-88738-220-7
  • The Hidden Hand: Middle East Fears of Conspiracy (1997), Palgrave Macmillan; paperback (1998) ISBN 0-312-17688-0
  • Conspiracy : How the Paranoid Style Flourishes and Where It Comes From (1997), Touchstone; paperback (1999) ISBN 0-684-87111-4
  • Syria Beyond the Peace Process (Policy Papers, No. 41) (1995), Washington Institute for Near East Policy, ISBN 0-944029-64-7
  • Sandstorm (1993), Rowman & Littlefield, paperback (1993) ISBN 0-8191-8894-8
  • Damascus Courts the West: Syrian Politics, 1989–1991 (Policy Papers, No. 26) (1991), Washington Institute for Near East Policy, ISBN 0-944029-13-2
  • with Garfinkle, A. (1991), Friendly Tyrants: An American Dilemma Palgrave Macmillan, ISBN 0-312-04535-2
  • The Rushdie Affair: The Novel, the Ayatollah, and the West (1990), Transaction Publishers, paperback (2003) ISBN 0-7658-0996-6
  • Greater Syria: The History of an Ambition (1990), Oxford University Press, ISBN 0-19-506021-0
  • In the Path of God: Islam and Political Power (1983), Transaction Publishers, ISBN 0-7658-0981-8
  • An Arabist's guide to Colloquial Egyptian (1983), Foreign Service Institute
  • Slave Soldiers and Islam: The Genesis of a Military System (1981), Yale University Press, ISBN 0-300-02447-9