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Novels
- Born to Exile (1978)
- In the Hands of Glory (1981)
- In the Red Lord's Reach (1989)
- Shadow of Earth (1979)
- Sorcerer's Son (1979)
- The City in Stone (unpublished)
- The Crystal Palace (1988)
- The Book of Elementals, Vol. 1 and 2 (2003) [O/1,2]
- Spec-Lit (1997)
- Spec-Lit 2 (1998)
- Conspicuous SF (2009)
- Walker Between the Worlds: A Fantasy Novella (2007)
- Altar Ego (1977) with Alex Eisenstein
- Attachment (1974)
- Beyond the Red Lord's Reach (1988)
- Boltzmann Schiaparelli and the Lizard King (2009)
- Born to Exile (1971)
- Boxes (1998)
- Dark Wings (1982)
- Dust in the Attic (1998)
- Fair Exchange (1985)
- In Answer to Your Call (1978)
- In the Western Tradition (1981)
- Inn of the Black Swan (1972)
- Lost and Found (1978)
- Nightlife (1982)
- No Refunds (1994)
- Point of Departure (1981)
- Sense of Duty (1985)
- Sleeping Beauty: The True Story (1976) with Alex Eisenstein
- Subworld (1983)
- Taboo (1981)
- Teleprobe (1974)
- The Amethyst Phial (1984)
- The Caravan to Nowhere (2014)
- The Cat (1998)
- The City of Lost Desire (2019)
- The Demon Queen (1984)
- The Desert of Vanished Dreams (2016)
- The Fireman's Daughter (1981)
- The Island in the Lake (1998)
- The Land of Sorrow (1977)
- The Last Golden Thread (2009)
- The Lords of All Power (1975)
- The Man with the Eye (1978)
- The Mountain Fastness (1979)
- The Park (1998)
- The Robe (1998)
- The Snail Out of Space (1985)
- The Sunstone (2013)
- The Trouble with the Past (1971) with Alex Eisenstein
- The Weather on Mars (1974) with Alex Eisenstein
- The Witch and the Well (1974)
- Tree of Life (1975)
- Von Neumann's Bug (2010) with Alex Eisenstein
- Walker Between the Worlds (2007)
- Wallpaper World (2001) with Alex Eisenstein
- Weaseling Out (1987)
- Wild Animals (1998)
- You Are Here (1977) with Alex Eisenstein
- Afterword (The Last Golden Thread) (2009)
- Afterword (Von Neumann's Bug) (2010) with Alex Eisenstein
- An Appreciation of Algis Budrys (2008) with Alex Eisenstein
- Auntie Anne's Sweet Sour Meetballs (1996)
- Bulletin Symposium (The Bulletin of the Science Fiction Writers of America, Winter 1985) (1985) with Brian W. Aldiss and Isaac Asimov and Michael Bishop and C. J. Cherryh and Arthur C. Clarke and Richard Cowper and L. Sprague de Camp and Fritz Leiber and Anne McCaffrey and Andre Norton and Brian Stableford and Jack Williamson
- Dubuqon (1978)
- Editorial (Spec-Lit 2) (1998)
- Editorial: Into the Unknown (Spec-Lit) (1997)
- Frederik Pohl, Science Fiction Grand Master (2004)
- Hoisin-Marinated Pork Chops (1996)
- Introduction: Promises Fulfilled: The work of Carol Emshwiller (2011)
- Introduction: Straddling the Spectrum (2003)
- Letter (Analog, March 1992) (1992)
- Letter (Locus #219) (1979) with Alex Eisenstein
- Letter (Locus #321) (1987)
- Letter (Locus #438) (1997)
- Letter (Vector 99) (1980)
- Letter to The SFWA Forum # 31, September 1973 (1973)
- Phyllis Eisenstein's Guide to Chicago (1991)
- Read This (NYRSF, February 1989) (1989)
- Read This (NYRSF, November 1996) (1996)
- Science Fiction and Me (1982)
- The Long and the Short of It (1968)
- The Pornographic Soapbox (1969)
- Where to Meet Pros and What to Do When You Get There (1982)
- Affair with a Green Monkey (1968) by Theodore Sturgeon
- The Annotated Guide to Startling Stories (1987) by Leon L. Gammell
- The Reincarnation of Peter Proud (1975) by Max Ehrlich
- Phyllis Eisenstein Interview (1999) by uncredited