Koja is also a prolific author of short stories, including many in collaboration with Barry N. Malzberg. Most of her short fiction remains uncollected. Koja's novels and short stories frequently concern characters who have been in some way marginalized by society, often focusing on the transcendence and/or disintegration which proceeds from this social isolation (as in The Cipher, Bad Brains, "Teratisms," The Blue Mirror, etc.). Koja won the Bram Stoker Award and the Locus Award for her first novel The Cipher, and a Deathrealm Award for Strange Angels. Her prose has been described as "stunning".
Koja's literary works have been recognized and highlighted at Michigan State University in their Michigan Writers Series.
- The Cipher (1991)
- Bad Brains (1992)
- Skin (1993)
- Strange Angels (1994)
- Kink (1996)
- Extremities (1997) (collection)
- Under the Poppy (2010)
- The Mercury Waltz (2014)
- Straydog (2002)
- Buddha Boy (2003)
- The Blue Mirror (2004)
- Talk (2005)
- Going Under (2006)
- Kissing the Bee (2007)
- Headlong (2008)
- Steffen Hantke, "Kathe Koja" in: Richard Bleiler, Ed. Supernatural Fiction Writers: Contemporary Fantasy and Horror. New York: Thomson/Gale, 2003. p. 541-550. ISBN 9780684312507
- "Novels & Stories | Writing about writing". Kathe Koja. Retrieved 2013-05-21.
- S. Kay Elmore (1998). "The SF Site Featured Review: Extremities". Sfsite.com. Retrieved 2013-05-21.
- Koja, Kathe. "Kathe Koja | Authors | Macmillan". Us.macmillan.com. Retrieved 2013-05-21.
-  Archived December 6, 2008, at the Wayback Machine.
- "Michigan Writers Series". Michigan State University Libraries. Retrieved 2012-07-15.
- http://www.freep.com/story/entertainment/arts/2014/10/22/ferndale-theater-halloween/17683097/. Missing or empty
- "The Locus Index to SF Awards: Index of Literary Nominees". Locus Magazine. Retrieved 2013-05-21.