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Novels
- Cities of the Red Night (1981)
- Dead Fingers Talk (1963)
- La machine molle [French] (1971)
- Le festin nu [French] (1964) with William Burroughs
- Le ticket qui explosa [French] (1972)
- My Education: A Book of Dreams (1995)
- Naked Lunch (1959)
- Naked Lunch [German] (1962)
- Naked Lunch (2005) with William Burroughs
- Naked Lunch [German] (2009)
- Nova Express (1964)
- Nova Express (1969) with William Burroughs
- Nova Express [French] (1972)
- Nova-Express [German] (1970)
- Port of Saints (1973)
- The Naked Lunch (1959) with William Burroughs
- The Place of Dead Roads (1984)
- The Soft Machine (1961)
- The Soft Machine (2010) with William Burroughs
- The Soft Machine: The Restored Text (2014)
- The Ticket That Exploded (1962)
- The Ticket That Exploded (1962) with William Burroughs
- The Western Lands (1987)
- The Wild Boys: A Book of the Dead (1971)
- Exterminator! (1973)
- Interzone (1989)
- Roosevelt After Inauguration and Other Atrocities (1979)
- The Exterminator (1960) with Brion Gysin
- The Exterminator (1960) with William Burroughs and Brion Gysin
- Blade Runner (a Movie) (1979)
- The Cat Inside (1986)
- Letters to Allen Ginsberg: 1953-1957 (1982)
- Letters to Allen Ginsberg: 1953-1957 (1982) with William Burroughs
- The Adding Machine: Collected Essays (1985)
- The Yage Letters (1975) with Allen Ginsberg
- "Exterminator!" (1973)
- "Johnny 23" (1973)
- "My Legs Señor" (1973)
- "What Washington? What Orders?" (1973)
- Ali's Smile (1973)
- Astronaut's Return (1973)
- Blade Runner (a Movie) (1979)
- Chapter Twenty-Eight of the Original "Junk" Manuscript (unknown)
- Crab Nebula (1964)
- Death Fiend Guerillas (1993)
- Electricals (1973)
- Exterminator (1960)
- Exterminator (1972) with William Burroughs
- Friends (1973)
- From Here to Eternity (1973)
- Fun City dans Ba'Dan [French] (1978)
- Ginsberg Notes (1989)
- Immortality (1981)
- International Zone (1989)
- Iron Wrack Dream (1989)
-
Kammerjäger?Kammerjaeger[German] (1976)
- L'exterminateur [French] (1969)
- Mother and I Would Like to Know (from The Wild Boys) (1991)
- My Face (1973)
- Naked Lunch (Outtakes) (2001)
- Old Movie (1973)
- Parler pour Joe [French] (1977) with William Burroughs
- Reddies (1973)
- Roosevelt After Inauguration (1979)
- Ruski (1984)
- Ruski [French] (1999)
- Seeing Red (1973)
- Short Trip Home (1973)
- Sput (1973)
- The "Priest" They Called Him (1973)
- The CIA Register (1989)
- The Coming of the Purple Better One (1973)
- The Conspiracy (1989)
- The Drums of Death (1973)
- The End (1973)
- The Ghost Lemurs of Madagascar (1987)
- The Lemon Kid (1973)
- The New Boy (1989)
- The Perfect Servant (1973)
- The Place of Dead Roads (excerpt) (1984)
- The Teacher (1973)
- They Do Not Always Remember (1966)
- They Do Not Always Remember (1966) with William Burroughs
- To Talk for Joe (1977)
- Twilight's Last Gleamings (1973)
- Twilight's Last Gleamings (1989)
- Wind Die You Die We Die (1968)
- Wind Die. You Die. We Die. (1973)
- Word (1989)
- Cold Lost Marbles (1973)
- The Evening News (1973)
- "Introduction" to the Original "Junk" Manuscript (unknown)
- Afterthoughts on a Deposition (1992)
- Behind-ForeEverAfterword: Sects and Death (1990)
- Brief eines Mannes, der gefährlichen Drogen verfallen war [German] (1995)
- Civilian Defense (1981)
- Deposition: Testimony Concerning a Sickness (1960)
- Eidesstattliche Erklärung: Aussagen über den Verlauf einer Krankheit [German] (1995)
- Glossary (Junky) (unknown)
- Introduction (Everything Is Permitted: The Making of Naked Lunch) (1991)
- Introduction (The Last Museum) (1986)
- Letter from a Master Addict to Dangerous Drugs (1956)
- Letter from William Burroughs to A. A. Wyn (unknown)
- Letter to Irving Rosenthal (1960)
- Post Script ... Wouldn't You? (1960)
- Preface (Love & Napalm: Export U.S.A.) (1972)
- Preface (The Atrocity Exhibition) (1972)
- Preface (The Atrocity Exhibition) (1980) with William Burroughs
- Prefazione (La mostra delle atrocità) [Italian] (1995) with William Burroughs
- Prologue (Junky) (unknown)
- Préface à l'édition américaine de 1990 [French] (2003) with William Seward Burroughs
- Roosevelt After Inauguration: A New Introduction (1979)
- Sects and Death (1979)
- The Death of Mel the Waiter (1953)
- The Whole Tamale (1979)
- When Did I Stop Wanting to Be President? (1979)
- Exterminator! (1985) with Steven Lowe
- Interzone (1989)
- My Education: A Book of Dreams (1995)
- Queer (unknown)
- The Soft Machine (1966)
- An Interview with William S. Burroughs (1990) by Larry McCaffery
- Interview with William S. Burroughs (1990) by Gregory Daurer
- The Hallucinatory Operators Are Real (1965) by uncredited
- The Hallucinatory Operators Are Real (1965) by SFH
- William S. Burroughs (1983) by Charles Platt
Non-Genre Titles
Novels
- And the Hippos Were Boiled in Their Tanks (2008) with Jack Kerouac
- Junkie (1953) with William Lee
- Junkie (1964) with William Burroughs
- Junky (1953)
- Queer (1985)
- Junkie / Narcotic Agent (1953) [O]
- Junkie / Narcotic Agent (1953) [O] with William Lee
- An Advertising Short for Television (1989)
- Antonio the Portuguese Mooch (1989)
- Davy Jones (1973)
- Displaced Fuzz (1989)
- Dream of the Penal Colony (1989)
- Driving Lesson (1989)
- End of the Line (1973)
- In the Café Central (1989)
- Lee and the Boys (1989)
- Lee's Journals (1989)
- Spare Ass Annie (1989)
- The Cat Inside (1986)
- The Discipline of DE (1973)
- The Dream Cops (1989)
- The Finger (1989)
- The Junky's Christmas (1989)
- Appendix (Queer) (1985)
- Introduction (Queer) (1985)