- Cosmic Trigger trilogy (1977-1979)
- The Illuminatus! trilogy (1975, written with Robert Shea)
- Schrodinger's Cat trilogy (1979-1981, written with Robert Shea)
- Prometheus Rising (1983)
- Quantum Psychology (1985, with Timothy Leary)
- Neuropolitics (1986)
- Sex and Drugs (1987, with Timothy Leary)
- Cosmic Laughter: The Lost Worlds of Robert Anton Wilson (1998, edited by Robert Shea)