From 1990 to 1997, Gonick penned a bimonthly "Science Classics" cartoon for the science magazine Discover. Each two-page comic discussed a recent scientific development, often one in interdisciplinary research. During the 1994-95 academic year, Gonick was a Knight Science Journalism Fellow at MIT[1]. In 1997, his 14-issue series, Candide in China, published on the World Wide Web, described Chinese inventions. He also writes the Kokopelli & Company comic that appears in the magazine Muse.

He drew the satirical, anti-corporate comic Commoners for Common Ground and later explained:

Feeling alternately mournful and enraged about the shameless expropriation of public space, public enterprise, publicly held goods like the atmosphere, oceans, and rivers, not to mention roads, parks, sidewalks, genomes, and the broadcast spectrum...indeed the very idea of the common good...I decided to do something about it! Well, say something, anyway.

Since early 2009 Gonick has also drawn a humorous webcomic entitled Raw Materials that deals with technology and business matters, especially database administration.

• Blood from a Stone : A Cartoon Guide to Tax Reform (with Steve Atlas)

(New York Public Interest Research Group, 1977(?)), ASIN B0006X9JW6

• The Cartoon Guide to Genetics (with Mark Wheelis)

(Barnes & Noble, 1983; revised edition, Collins, 1991), ISBN 0-06-273099-1

• The Cartoon History of the Universe - From the Big Bang to Alexander the Great (Volumes 1-7)

(Doubleday, 1990), ISBN 0-385-26520-4

• The Cartoon Guide to the Computer (originally The Cartoon Guide to Computer Science)

(reprint edition, Collins, 1991), ISBN 0-06-273097-5

• The Cartoon History of the United States

(revised edition, Collins, 1991), ISBN 0-06-273098-3

• The Cartoon Guide to Physics (with Art Huffman)

(reprint edition, Collins, 1992), ISBN 0-06-273100-9

• The Cartoon Guide to (non)Communication

(reprint edition, Collins, 1993), ISBN 0-06-273217-X

• The Cartoon Guide to Statistics (with Woollcott Smith)

(Collins, 1994), ISBN 0-06-273102-5

• The Cartoon History of the Universe II - From the Springtime of China to the Fall of Rome (Volumes 8-13)

(Doubleday, 1994), ISBN 0-385-42093-5

• The Cartoon Guide to the Environment (with Alice Outwater)

(Collins, 1996), ISBN 0-06-273274-9

• The Cartoon Guide to Sex (with Christine Devault)

(Collins, 1999), ISBN 0-06-273431-8

• The Cartoon History of the Universe III - From the Rise of Arabia to the Renaissance (Volumes 14-19)

(Doubleday, 2002), ISBN 0-393-05184-6

• Kokopelli and Company in Attack of the Smart Pies (fiction)

(Cricket Books, 2005), ISBN 0-8126-2740-7

• The Cartoon Guide to Chemistry (with Craig Criddle)

(Collins, 2005), ISBN 0-06-093677-0

• The Cartoon History of the Modern World, Volume 1: From Columbus to the U.S. Constitution

(Collins, 2007), ISBN 0-06-076004-4

• The Cartoon History of the Modern World, Volume 2: From the Bastille to Baghdad

(Collins, 2009), ISBN 0-06-076008-7