• Livro de seres invisiveis (2021)ISBN 9786588069035
• Cosmic Apprentice: Dispatches from the Edges of Science (2013) ISBN 978-0-8166-8135-8
• Lynn Margulis: The Life and Legacy of a Scientific Rebel (2012, Sciencewriters Books) ISBN 1603584463
• Death and Sex (two-in-one book with Tyler Volk, 2009) ISBN 1-60358-143-X
• Biospheres: Metamorphosis of Planet Earth (1990) ISBN 0-07-054426-3
• Notes from the Holocene: A Brief History of the Future (2007) ISBN 1-933392-32-0
• Cooking with Jesus: From the Primal Brew to the Last Brunch (2001) ISBN 1-58898-160-6
• The Sciences of Avatar (2010) ASIN B004089DDI

Co-written with Lynn Margulis

• Microcosmos: Four Billion Years of Evolution from Our Microbial Ancestors (1986) ISBN 0671441698
• Origins of Sex : Three Billion Years of Genetic Recombination (1986) ISBN 978-0300046199
• Garden of Microbial Delights: A Practical Guide to the Subvisible World (1988) ISBN 978-0787201364
• Biospheres from Earth to Space ISBN 978-0894901881 (1989)
• Mystery Dance: On the Evolution of Human Sexuality ISBN 978-0671792268 (1991)
• What Is Sex? ISBN 978-0684826912 (1995)
• What Is Life? (1995) ISBN 0684810875
• Slanted Truths: Essays on Gaia, Symbiosis, and Evolution (1997)
• Acquiring Genomes: A Theory of the Origins of Species (2002) ISBN 0465043925
• Dazzle Gradually: Reflections on the Nature of Nature (2007) ISBN 1933392312

Co-written with Eric D. Schneider

• Into the Cool: Energy Flow, Thermodynamics, and Life (2005) ISBN 0226739368

Co-written with others

• Cracking the Aging Code: The New Science of Growing Old - And What It Means for Staying Young (2016 - with Josh Mitteldorf)
• Up From Dragons: The Evolution of Human Intelligence (2002 - with John Skoyles)
• Within the Stone: Nature's Abstract Rock Art (2004 - partial text to book of photographs by Bill Atkinson)
• Atheist Universe: The Thinking Person's Answer to Christian Fundamentalism (2006 - foreword to book by David Mills)
• Darwin's Unfinished Business: The Self-Organizing Intelligence of Nature (2011 - with Simon G Powell)

• "Möbius Trip: The Technosphere and Our Science Fiction Reality" Technosphere Magazine (2017)
• "Metametazoa: Biology and Multiplicity" (1992 - In Incorporations: Fragments for a History of the Human Body, Jonathan Crary and Sanford Kwinter, editors, Zone, pp. 362–385)
• "Partial closure: Dorion Sagan reflects on Carl" (1997 - Whole Earth, summer, pp. 34–37)
• "Gender Specifics: Why Women Aren't Men" (1998 - The New York Times )
• "The Beast with Five Genomes" (2001 - with Lynn Margulis - Natural History June, pp. 38–41)
• "The Postman Already Always Rings Twice: Fragments for an Understanding of the Future" (2004 Cabinet: A Quarterly of Art and Culture, pp. 23–27)
• "Gradient-Reduction Theory: Thermodynamics and the Purpose of Life" (2004 - with Jessica H. Whiteside. In Scientists Debate Gaia: The Next Century MIT Press)
• "A Brief History of Sex" (2007 - Cosmos [Australia], June/July, pp. 50–55)
• "Evolution, Complexity, and Energy Flow" (2008 - Back to Darwin: A Richer Account of Evolution John B. Cobb Jr., Editor, William B. Eerdmans Publishing Company, pp. 145–156)
• "What is the Cultural Relevance of Bacteria?" (2009 - Sputnik Observatory)

• "The Tchaikovsky Dream Continuum" Cabinet, Issue 54 The Accident (Summer 2014)
• "The New Age Witch" (1993) After Hours, #19, summer, pp. 36–45
• "Love’s Strangers" (2006) Meat for Tea: The Northampton Review, summer, Vol. 1, Issue 3, "Flesh," pp. 3–10
• "Semi-Naked" (2006) Meat for Tea: The Northampton Review, winter, Vol. 1, Issue 1, "Gristle," pp. 5–24