| The Jewels of Aptor | 1962 |
| Captives of the Flame | 1963 |
| The Towers of Toron | 1964 |
| City of a Thousand Suns | 1965 |
| Babel 17: Empire Star | 1966 |
| The Einstein Intersection | 1967 |
| Nova | 1968 |
| The Fall of the Towers | 1970 |
| Quark/1 | 1970 |
| Driftglass | 1971 |
| Quark/2 | 1971 |
| Quark/3 | 1971 |
| Quark/4 | 1971 |
| Dhalgren | 1975 |
| Trouble on Triton: An Ambiguous Heterotopia | 1976 |
| The Jewel-Hinged Jaw | 1977 |
| The American Shore | 1978 |
| Nebula Winners 13 | 1979 |
| Tales of Neveryon | 1979 |
| Distant Stars | 1981 |
| Starboard Wine | 1984 |
| Stars in My Pocket Like Grains of Sand | 1984 |
| Flight from Neveryon | 1985 |
| The Complete Nebula Award-Winning Fiction | 1986 |
| Neveryona | 1986 |
| The Bridge of Lost Desire | 1987 |
| The Motion of Light in Water | 1988 |
| Wagner/Artaud: A Play of 19th and 20th Century Critical Fictions | 1988 |
| The Best of the Nebulas | 1989 |
| The Straits of Messina | 1989 |
| Driftglass/Starshards | 1993 |
| They Fly at Ciron | 1993 |
| Equinox | 1994 |
| The Mad Man | 1994 |
| Silent Interviews: On Language, Race, Sex, Science Fiction and Some Comics | 1994 |
| Atlantis: Three Tales | 1995 |
| Hogg | 1995 |
| Longer Views | 1996 |
| Bread & Wine: An Erotic Tale of New York | 1999 |
| Shorter Views | 1999 |
| 1984: Selected Letters | 2000 |
| Aye, and Gomorrah: And Other Stories | 2003 |
| Masters of the Pit | 2008 |