* *Too Hot to Handle: The Race for Cold Fusion* (1992)
* *China Steam: A Cultural History of Chinese Railways* (1994)
* *A New History of Christianity: Exploring Modern Christianities and the Transformation of the West* (1996)
* *The New Atheism* (2007)
* *Jesus: The Evidence* (2009)
* *The Birth of Jesus: A New Investigation* (2010)
* *The Historical Jesus: A Comprehensive Guide* (2011)
* *The Resurrection of Jesus: A New Historiographical Approach* (2012)
* *The Jesus Mystery: Twelve Questions That Challenge the Traditional View* (2013)
* *The Gospels and Jesus* (2014)
* *The Parables of Jesus* (2015)
* *The Miracles of Jesus* (2016)
* *Christian Fundamentalism: A Guide for the Perplexed* (2017)
* *An Introduction to Christianity: A Global Perspective* (2018)
* *The Future of Christianity* (2019)
Fiction:
* *The Edge of Reason* (2004)
* *The Fifth Gospel* (2006)
* *The Secret Gospel* (2008)
* *The Pauli Exclusion Principle: A Novel* (2011)
* *The Turing Enigma: A Novel* (2014)
* *The Heretic's Apprentice: A Novel* (2017)
* *The Heretic Queen: A Novel* (2019)