Books

• A Conscientious Guide to Hallucinogens: A Comprehensive Guide to Hallucinogens, Natural and Synthetic, Found in North American and the World with Joe E Axton and Jeremy Bigwood (1975) Do It Now Foundation, Institute for Chemical Survival
• Hallucinogenic Plants of North America (1976), ISBN 0-914728-16-4
• Teonanacatl: Hallucinogenic Mushrooms of North America (Co-edited by Jeremy Bigwood) (1978), ISBN 0-914842-32-3
• LSD: My Problem Child (1980) McGraw-Hill Book Company ISBN 0-07-029325-2 (translation only)
• The Cacahuatl Eater: Ruminations of an Unabashed Chocolate Addict (Natural Products Company) (1985) ISBN 0-9614234-1-2
• Persephone's Quest: Entheogens and the Origins of Religion with R. Gordon Wasson, Stella Kramrisch, and Carl A. P. Ruck (1986) ISBN 0-300-05266-9
• The Sacred Mushroom Seeker: Essays for R. Gordon Wasson? by Robert Gordon Wasson, Thomas J. Riedlinger (1990) contributor
• Pharmacotheon: Entheogenic Drugs, Their Plant Sources and History (1993), ISBN 0-9614234-2-0
• Ayahuasca Analogues: Pangaean Entheogens (1995), ISBN 0-9614234-4-7
• Plant Intoxicants: a Classic Text on the Use of Mind-Altering Plants? by Ernst Bibra and Jonathan Ott (1995) Nature
• Age of Entheogens & the Angels' Dictionary (1995), ISBN 0-9614234-6-3
• Pharmacophilia: The Natural Paradise (1997), ISBN 1-888755-00-8
• Shamanic Snuffs or Entheogenic Errhines (2001), ISBN 1-888755-02-4
• Ometochtzin: Las Muertes de Dos Conejos (2001)
• Drugs of the Dreaming: Oneirogens: Salvia Divinorum and Other Dream-Enhancing Plants with Gianluca Toro and Benjamin Thomas (2007) Body, Mind & Spirit
• The Road to Eleusis (2008) By R. Gordon Wasson, Albert Hofmann, Carl A. P. Ruck, Huston Smith (contributor)

Articles

• Ethnopharmacognosy and Human Pharmacology of Salvia divinorum and Salvinorin A (1995)
• Pharmahuasca: On Phenethylamines and Potentiation (1996)
• Pharmahuasca, Anahuasca and Vinho da Jurema: Human Pharmacology of Oral DMT Plus Harmine (1997)
• The Delphic Bee: Bees and Toxic Honeys as Pointers to Psychoactive and Other Medicinal Plants - Economic Botany (1998)
• Applied Psychonautics: Ayahuasca to Pharmahuasca to Anahuasca (2001)
• Pharmanopo-Psychonautics: Human Intranasal, Sublingual, Intrarectal, Pulmonary and Oral Pharmacology of Bufotenine (2001)
• Jonathan Ott's victim of arson, signed copies of Albert Hofmann books used to start fire (2010)

• Jonathan Ott at the World Psychedelic Forum [part 1 of 5