| # | Title | Release Date | Label | Type | UK | USA |
| 1. | School | 1979 | | | | |
| 2. | Pool | 1980 | | | | |
| 3. | Archery | 1981 | | | | |
| 4. | Yankees
& Derek Bailey & George Lewis | 1983 | | | | |
| 5. | The Classic Guide To Strategy
(2LP) | 1984 | |  | | |
| 6. | Ganryu Islands | 1984 | | | | |
| 7. | Lolus Solus
credited to: John Zorn's Experimental Rock Trios | 9/1984 | Rift | | | |
| 8. | The Big Gundown | 1985 | | | | |
| 9. | Torture Garden | 1989 | | | | |
| 10. | Naked City | 1989 | 1972 | | | |
| 11. | Spy vs. Spy: The Music of Ornette Coleman | 1989 | Music on Vinyl | | | |
| 12. | Filmworks | 1990 | | | | |
| 13. | Elegy | 1992 | | | | |
| 14. | Kristallnacht | 1993 | | | | |
| 15. | Live At The Knitting Factory
credited to: John Zorn's Cobra
(live) | 4/1995 | Knitting Factory |  | | |
| 16. | Masada 10 | 16.11.1998 | | | | |
| 17. | Masada Live In Jerusalem
& Masada
(live) | 20.04.1999 | | | | |
| 18. | Masada Live in Taipei
& Masada
(live) | 18.05.1999 | | | | |
| 19. | 50th Birthday, Vol. 5
& Fred Frith | 27.07.2004 | Tzadik | | | |
| 20. | 50th Birthday Celebration, Vol. 7 | 21.09.2004 | Tzadik | | | |
| 21. | 50th Birthday Celebration, Vol. 8
& Wadada Leo Smith & Susie Ibarra | 09.11.2004 | Tzadik | | | |
| 22. | Naninani II
& Yamataka Eye | 09.11.2004 | Tzadik | | | |
| 23. | 50th Birthday Celebration, Vol. 10
& Yamataka Eye | 25.01.2005 | Tzadik | | | |
| 24. | Rituals | 22.02.2005 | Tzadik | | | |
| 25. | Film Works, Vol. 15 | 08.03.2005 | Tzadik | | | |
| 26. | Best of Filmworks: 20 Years of Soundtrack Music | 23.08.2005 | Tzadik | | | |
| 27. | At the Mountain of Madness: Live in Europe
& Electric Masada
(live) | 22.11.2005 | Tzadik | | | |
| 28. | Film Works, Vol. 17: Notes on Marie Menken | 24.01.2006 | Tzadik | | | |
| 29. | Moonchild | 23.05.2006 | Tzadik | | | |
| 30. | Astronome | 17.10.2006 | Tzadik | | | |
| 31. | Six Litanies for Heliogabalus | 27.03.2007 | Tzadik | | | |
| 32. | Film Works, Vol. 19: The Rain Horse | 22.01.2008 | Tzadik | | | |
| 33. | Dreamers | 18.03.2008 | Tzadik | | | |
| 34. | Bar Kokhba: Lucifer - Book Of Angels Vol 10 | 24.03.2008 | Tzadik | | | |
| 35. | Filmworks, Vol. 20: Sholem Aleichem | 16.09.2008 | Tzadik | | | |
| 36. | Film Works, Vol. 21: Belle de Nature / Rijksmuseum | 28.10.2008 | Tzadik | | | |
| 37. | Crucible | 25.11.2008 | Tzadik | | | |
| 38. | Film Works, Vol. 22: The Last Supper | 25.11.2008 | Tzadik | | | |
| 39. | Film Works, Vol. 23: General | 24.02.2009 | Tzadik | | | |
| 40. | Alhambra Love Songs | 18.05.2009 | Tzadik | | | |
| 41. | Music For Children
(remastered) | 11.06.2009 | Tzadik | | | |
| 42. | O'o | 28.07.2009 | Tzadik | | | |
| 43. | Ipos: The Book of Angels, Vol. 14
& The Dreamers | 23.03.2010 | Tzadik | | | |
| 44. | Late Works
& Fred Frith | 05.05.2010 | Tzadik | | | |
| 45. | The Goddess: Music for the Ancient of Days | 29.06.2010 | Tzadik | | | |
| 46. | Filmworks, Vol. 24: The Nobel Prize Winner | 24.08.2010 | Tzadik | | | |
| 47. | Ipsissimus | 05.10.2010 | Tzadik | | | |
| 48. | John Zorn: Interzone | 09.11.2010 | Tzadik | | | |
| 49. | Zorn: Nova Express | 22.03.2011 | Tzadik | | | |
| 50. | At the Gates of Paradise | 27.09.2011 | Tzadik | | | |
| 51. | A Dreamer's Christmas | 11.10.2011 | Tzadik | | | |
| 52. | Mount Analogue | 31.01.2012 | Tzadik | | | |
| 53. | Gnostic Preludes | 13.03.2012 | Tzadik | | | |
| 54. | John Zorn: Nosferatu | 24.04.2012 | Tzadik | | | |
| 55. | Templars: In Sacred Blood | 22.05.2012 | Tzadik | | | |
| 56. | The Hermetic Organ | 19.06.2012 | Tzadik | | | |
| 57. | Abraxas: The Book of Angels, Vol. 19
& Shanir Ezra Blumenkranz | 31.07.2012 | Tzadik | | | |
| 58. | A Vision in Blakelight | 25.09.2012 | Tzadik | | | |
| 59. | The Concealed | 27.11.2012 | Tzadik | | | |
| 60. | John Zorn: The Mysteries
& Carol Emanuel & Bill Frisell & Kenny Wollesen | 26.03.2013 | Tzadik | | | |
| 61. | Dreamachines | 20.07.2013 | Tzadik | | | |
| 62. | @
& Thurston Moore | 24.09.2013 | Tzadik | | | |
| 63. | In Lambeth: Visions from the Walled Garden of William Blake
& Gnostic Trio | 22.10.2013 | Tzadik | | | |
| 64. | The Hermetic Organ, Vol. 2 | 21.01.2014 | Tzadik | | | |
| 65. | Psychomagia | 18.02.2014 | Tzadik | | | |
| 66. | Fragmentations, Prayers, and Interjections | 18.03.2014 | Tzadik | | | |
| 67. | In the Hall of Mirrors | 27.05.2014 | Tzadik | | | |
| 68. | Sonic Rivers
& George Lewis & Wadada Leo Smith | 24.06.2014 | Tzadik | | | |
| 69. | From Leaves of Grass | 22.07.2014 | Tzadik | | | |
| 70. | Adramelech: The Book of Angels, Vol. 22
& Zion80 | 22.07.2014 | Tzadik | | | |
| 71. | The Testament of Solomon | 19.08.2014 | Tzadik | | | |
| 72. | The Dream Membrane
& Bill Laswell & David Chaim Smith | 30.09.2014 | Tzadik | | | |
| 73. | Valentine's Day: John Zorn's Enigma Trios | 30.09.2014 | Tzadik | | | |
| 74. | Aguares: The Book of Angels, Vol. 23
& Roberto Rodriguez | 30.09.2014 | Tzadik | | | |
| 75. | The Last Judgment | 18.11.2014 | Tzadik | | | |
| 76. | John Zorn's Olympiad, Vol. 1: The Early Game Pieces
& Dither | 20.01.2015 | Tzadik | | | |
| 77. | The Hermetic Organ, Vol. 3: St. Paul's Hall, Huddersfield | 20.01.2015 | Tzadik | | | |
| 78. | John Zorn: Hen to Pan | 17.02.2015 | Tzadik | | | |
| 79. | Simulacrum | 17.03.2015 | Tzadik | | | |
| 80. | The Song Project: Live at LPR
(live) | 28.04.2015 | Tzadik | | | |
| 81. | Pellucidar: A Dreamers Fantabula
& The Dreamers | 23.06.2015 | Tzadik | | | |
| 82. | The True Discoveries of Witches and Demons | 21.08.2015 | Tzadik | | | |
| 83. | Inferno | 18.09.2015 | Tzadik | | | |
| 84. | Cerberus: The Book of Angels, Vol. 26 | 20.11.2015 | Tzadik | | | |
| 85. | Madrigals | 22.01.2016 | Tzadik | | | |
| 86. | The Hermetic Organ, Vol. 4: St. Bartholomew's | 22.01.2016 | Tzadik | | | |
| 87. | Flaga: The Book of Angels, Vol. 28 | 26.02.2016 | Tzadik | | | |
| 88. | Flaga: The Book of Angels, Vol. 27 | 18.03.2016 | Tzadik | | | |
| 89. | The Painted Bird | 18.03.2016 | Tzadik | | | |
| 90. | The Mockingbird | 22.04.2016 | Tzadik | | | |
| 91. | Flauros: The Book of Angels, Vol. 29
& Autoryno | 22.07.2016 | Tzadik | | | |
| 92. | John Zorn: Sacred Visions
& Jack Quartet | 22.07.2016 | Tzadik | | | |
| 93. | John Zorn: Commedia dell'Arte | 26.08.2016 | Tzadik | | | |
| 94. | 49 Acts of Unspeakable Depravity in the Abominable Life and Times of Gilles de Rais | 30.09.2016 | Tzadik | | | |
| 95. | Blink
& Yoko Ono | 01.10.2016 | Chimera Music | | | |
| 96. | The Classic Guide to Strategy, Vol. 4 | 04.11.2016 | Tzadik | | | |
| 97. | The Garden of Earthly Delights | 24.02.2017 | Tzadik | | | |
| 98. | There Is No Firmament | 24.03.2017 | Tzadik | | | |
