• The Japanese Tattoo (1980) with Donald Richie ISBN 978-0-8348-0228-5
• Behind the Mask: On Sexual Demons, Sacred Mothers, Transvestites, Gangsters, Drifters, and Other Japanese Cultural Heroes (1983) ISBN 978-0-452-00738-3
• Tokyo: Form and Spirit (1986) with James R. Brandon, Kenneth Frampton, Martin Friedman, Donald Richie
• God's Dust: A Modern Asian Journey (1989) ISBN 978-0-7538-1089-7
• Great Cities of the World: Hong Kong (1991)
• Playing the Game (1991) novel ISBN 978-0-374-52633-7
• The Wages of Guilt: Memories of War in Germany and in Japan (1994) ISBN 978-0-452-01156-4
• Geisha: The Life, the Voices, the Art (1998) with Jodi Cobb
• Voltaire's Coconuts, or Anglomania in Europe (UK title) (1998) or Anglomania: a European Love Affair (US title) (1999) ISBN 978-0-7538-0954-9
• The Missionary and the Libertine: Love and War in East and West (2000) compilation ISBN 978-0-571-21414-3
• De neo-romantiek van schrijvers in exil (Neoromanticism of writers in exile) (2000) ISBN 90-446-0028-1
• Bad Elements: Chinese Rebels from Los Angeles to Beijing (2001) ISBN 978-0-679-78136-3
• Inventing Japan: From Empire to Economic Miracle 1853—1964 (2003) ISBN 978-0-679-64085-1
• Occidentalism: The West in the Eyes of Its Enemies (2004) with Avishai Margalit ISBN 978-0-14-303487-2
• Murder in Amsterdam: The Death of Theo Van Gogh and the Limits of Tolerance (2006) ISBN 978-1-59420-108-0 winner of The Los Angeles Times Book Prize for the Best Current Interest Book.
• The China Lover (2008)novel ISBN 978-1-59420-194-3
• Taming the Gods: Religion and Democracy on Three Continents (2010) ISBN 978-0-691-13489-5, with some historical examples of the value the separation of religion and national governance with the separation of church and state as one example.
• Grenzen aan de vrijheid: van De Sade tot Wilders (Limits to Freedom: From De Sade to Wilders) (2010) — Essay for the Month of Philosophy in the Netherlands.

Essays

• China's class ceiling, published in the Los Angeles Times