1973 – Honest Prayer, ISBN 1-878282-18-2

1974 – This Hebrew Lord, ISBN 0-06-067520-9

1975 – Christpower, ISBN 1-878282-11-5

1975 – Dialogue: In Search of Jewish-Christian Understanding (co-authored with Rabbi Jack Daniel Spiro), ISBN 1-878282-16-6

1976 – Life Approaches Death: A Dialogue on Ethics in Medicine

1977 – The Living Commandments, ISBN 1-878282-17-4

1980 – The Easter Moment, ISBN 1-878282-15-8

1983 – Into the Whirlwind: The Future of the Church, ISBN 1-878282-13-1

1986 – Beyond Moralism: A Contemporary View of the Ten Commandments (co-authored with Denise G. Haines, Archdeacon), ISBN 1-878282-14-X

1987 – Consciousness and Survival: An Interdisciplinary Inquiry into the possibility of Life Beyond Biological Death (edited by John S. Spong, introduction by Claiborne Pell), ISBN 0-943951-00-3

1988 – Living in Sin? A Bishop Rethinks Human Sexuality, ISBN 0-06-067507-1

1991 – Rescuing the Bible from Fundamentalism: A Bishop Rethinks the Meaning of Scripture, ISBN 0-06-067518-7

1992 – Jesús, hijo de mujer, Barcelona, 1993. ISBN 84-270-1705-7 (agotado). (Born of a Woman: A Bishop Rethinks the Birth of Jesus, ISBN 0-06-067523-3)

1994 – La Resurrección, ¿mito o realidad?, Barcelona, 1996. ISBN  84-270-2108-9 (agotado). (Resurrection: Myth or Reality? A Bishop's Search for the Origins of Christianity, ISBN 0-06-067546-2)

1996 – Liberating the Gospels: Reading the Bible with Jewish Eyes, ISBN 0-06-067557-8

1999 – Why Christianity Must Change or Die: A Bishop Speaks to Believers In Exile, ISBN 0-06-067536-5

2001 – Here I Stand: My Struggle for a Christianity of Integrity, Love and Equality, ISBN 0-06-067539-X

2002 – Un cristianismo nuevo para un mundo nuevo ISBN 978-994-209-004-1. Un novo cristianismo para um novo mundo: a fé além dos dogmas, Campinas, SP, Campinas, SP, 2006. ISBN 85-87795-97-X. (A New Christianity for a New World: Why Traditional Faith Is Dying and How a New Faith Is Being Born, ISBN 0-06-067063-0)

2005 – The Sins of Scripture: Exposing the Bible's Texts of Hate to Reveal the God of Love, ISBN 0-06-076205-5

2007 – Jesus for the Non-Religious, ISBN 0-06-076207-1

2009 – Eternal Life: A New Vision: Beyond Religion, Beyond Theism, Beyond Heaven and Hell, ISBN 0-06-076206-3

2011 - Re-Claiming the Bible for a Non-Religious World, ISBN 978-0-06-201128-2