Books published by Alyson include:
- Young, Gay and Proud (ISBN 1-55583-001-3), edited by Sasha Alyson and Lynne Yamaguchi Fletcher.
- The Dykes to Watch Out For cartoon series, by Alison Bechdel
- The Second Coming: A Leatherdyke Reader (ISBN 1-55583-281-4), edited by Pat Califia and Robin Sweeney
- Melting Point (ISBN 1-55583-162-1), short stories by Pat Califia
- Doing it for Daddy (ISBN 1-55583-227-X), short stories by Pat Califia
- Macho Sluts (ISBN 1-55583-115-X), erotic fiction by Pat Califia
- Doc and Fluff (ISBN 1-55583-176-1), a novel by Pat Califia
- Latter Days (ISBN 1-55583-868-5), novelization by T. Fabris for the 2003 major motion picture of the same name.
- The First Gay Pope and Other Records, by Lynne Yamaguchi Fletcher
- The Femme Mystique (ISBN 1-55583-255-5), short stories edited by Lesléa Newman
- Pillow Talk (ISBN 1-55583-419-1), short stories edited by Lesléa Newman
- The Lillian Byrd crime fiction series, by Elizabeth Sims
- Revolutionary Voices: A Multicultural Queer Youth Anthology (ISBN 1-55583-558-9), edited by Amy Sonnie.
- The Trouble with Harry Hay: Founder of the Modern Gay Movement, by Stuart Timmons
- Half-Life, a novel by Aaron Krach
- Out on Fraternity Row: Personal Accounts of Being Gay in a College Fraternity, by Shane Windmeyer
- Secret Sisters: Stories of Being Lesbian & Bisexual in a College Sorority
- Best Lesbian Love Stories, 2003-2005, edited by Angela Brown
- Mentsh: On Being Jewish and Queer, edited by Angela Brown
- Love, Bourbon Street: Reflections of New Orleans, edited by Greg Herren and Paul J. Willis—winner 2006 Lambda Literary Award for Anthology
- Bi Any Other Name: Bisexual People Speak Out (ISBN 1-55583-174-5), edited by Loraine Hutchins and Lani Ka'ahumanu
- The Bisexual's Guide to the Universe, by Michael Szymanski and Nicole Kristal—winner 2006 Lambda Literary Award for Bisexual
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