- "O'Brien and Obrenov" (1946)
- "Duo Miaule" (Ca. 1950s; Rediscovered/published 2008)
- The Lovers (1952) (expanded to novel of same name, 1961)
- "Sail On! Sail On!" (1952)
- "The Biological Revolt" (1953)
- "Mother" (1953)
- "Moth and Rust" (1953) (basis of novel, A Woman a Day (1960))
- "Attitudes" (1953)
- "Strange Compulsion" (1953)
- "They Twinkled Like Jewels" (1954)
- "Daughter" (1954)
- "Queen of the Deep" (1954)
- "The God Business" (1954)
- "Rastignac the Devil" (1954)
- "The Celestial Blueprint" (1954)
- "The Wounded" (1954)
- "Totem and Taboo" (1954)
- "Father" (1955)
- "The Green Odyssey" (1957)
- "The Night of Light" (1957)
- "The Alley Man" (1959)
- "Heel" (1960)
- "My Sister's Brother" or "Open to Me, My Sister" (1960)
- "A Few Miles" (1960)
- "Prometheus" (1961)
- "Tongues of the Moon" (1961) (expanded as novel of same name, 1964)
- "Uproar in Acheron" (1962)
- "How Deep the Grooves" (1963)
- "Some Fabulous Yonder" (1963)
- "The Blasphemers" (1964)
- "The King of the Beasts" (1964)
- "Day of the Great Shout" (1965)[9]
- "Riverworld" (1966)[10]
- "The Suicide Express" (1966)[11]
- "The Blind Rowers" (1967)
- "A Bowl Bigger than Earth" (1967)
- "The Felled Star (part 1)" (1967)
- "The Felled Star (part 2)" (1967)
- "The Shadow of Space" (1967)
- "Riders of the Purple Wage" (1967)
- "Don't Wash the Carats" (1968)
- "The Jungle Rot Kid on the Nod" (1968)
- "Down in the Black Gang" (1969)
- "The Oogenesis of Bird City" (1970)
- "The Voice of the Sonar in my Vermiform Appendix" (1971)
- "Brass and Gold" (1971)
- "The Fabulous Riverboat (part 1)" (1971)
- "The Fabulous Riverboat (part 2)" (1971)
- "Only Who Can Make a Tree?" (1971)
- "The Sliced-Crosswise Only-On-Tuesday World" (1971) (basis of the Dayworld series of novels)
- "Seventy Years of Decpop" (1972)
- "Skinburn" (1972)
- "The Sumerian Oath" (1972)
- "Father's in the Basement" (1972)
- "Toward the Beloved City" (1972)
- "Mother Earth Wants You" (1972)
| - "Sketches Among the Ruins of My Mind" (1973)
- "Monolog" (1973)
- "After King Kong Fell" (1973)
- "Opening the Door" (1973)
- "The Two-Edged Gift" (1974)
- "The Startouched" (1974)
- "The Evolution of Paul Eyre" (1974)
- "Passing On" (1975)
- "A Scarletin Study, as Jonathan Swift Somers III" (1975)
- "The Problem of the Sore Bridge - Among Others, as Harry Manders" (1975)
- "Greatheart Silver" (1975)
- "The Return of Greatheart Silver" (1975)
- "Osiris on Crutches, as Leo Queequeg Tincrowder" (1976)
- "The Volcano, as Paul Chapin" (1976)
- "The Doge Whose Barque Was Worse Than His Bight, as Jonathan Swift Somers III" (1976)
- "Fundamental Issue" (1976)
- "The Henry Miller Dawn Patrol" (1977)
- "Greatheart Silver in the First Command" (1977)
- "Savage Shadow as Maxwell Grant" (1977)
- "The Impotency of Bad Karma as Cordwainer Bird" (1977)
- "It's the Queen of Darkness, Pal, as Rod Keen" (1978)
- "Freshman" (1979)
- "The Leaser of Two Evils" (1979)
- "J.C. on the Dude Ranch" (1979)
- "Spiders of the Purple Mage" (1980)
- "The Making of Revelation, Part I" (1980)
- "The Long Wet Dream of Rip Van Winkle" (1981)
- "The Adventure of the Three Madmen" (1984) (rewrite of The Adventure of the Peerless Peer (1974))
- "UFO vs IRS" (1985)
- "St. Francis Kisses His Ass Goodbye" (1989)
- "One Down, One to Go" (1990)
- "Evil, Be My Good" (1990)
- "Nobody's Perfect" (1991)
- "Wolf, Iron and Moth" (1991)
- "Crossing the Dark River" (1992)
- "A Hole in Hell" (1992; as "Dane Helstrom")
- "Up the Bright River" (1993)
- "Coda" (1993)
- "The Good of the Land" (2002)
- "The Face that Launched a Thousand Eggs" (2005)
- "The Unnaturals" (2005)
- "Who Stole Stonehenge?" (2005)
- "That Great Spanish Author, Ernesto" (2006)
- "The Essence of the Poison" (2006)
- "The Doll Game" (2006)
- "Keep Your Mouth Shut" (2006)
- "The Frames" (2007)
- "A Spy in the U.S. of Gonococcia" (2007)
- "A Peoria Night" (2007)
- "The First Robot" (2008)
- "Getting Ready to Write" (2008) (co-authored with Paul Spiteri)
- "My Summer Husband" (2010)
- "What I Thought I Heard" (2011)
- "Kwasin and the Bear God" (2011) (co-authored with Christopher Paul Carey)
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