- 1960: Outward Bound (New Jazz)
- 1960: Out There (New Jazz)
- 1961: Far Cry (New Jazz)
- 1961: At the Five Spot, Vol. 1 (New Jazz) (live)
- 1964: Out to Lunch! (Blue Note)
Posthumous compilations
- 1959: Hot & Cool Latin
- 1959: Wherever I Go
- 1960: Candid Dolphy
- 1960: Status
- 1960: Dash One (Prestige)
- 1960: Fire Waltz
- 1960: Magic
- 1960: Other Aspects (Blue Note)
- 1960: Eric Dolphy
- 1961: Here and There
- 1961: Eric Dolphy in Europe, Vols. 1-3 (Prestige) also released as Copenhagen Concert (live)
- 1961: The Complete Uppsala Concert
- 1961: Stockholm Sessions
- 1961: Quartet 1961 also released as Softly, As in a Morning Sunrise (live)
- 1961: At the Five Spot, Vol. 2 (Prestige) (live)
- 1961: Memorial Album (Prestige) (live)
- 1962: Vintage Dolphy
- 1962: Eric Dolphy Quintet featuring Herbie Hancock: Complete Recordings
- 1962: Berlin Concerts (live)
- 1963: Iron Man
- 1963: Conversations (both Conversations and Iron Man were released as a double LP titled Jitterbug Waltz)
- 1963: The Illinois Concert (Blue Note) (live)
- 1964: Last Date (live)
- 1964: Naima
- 1964: Unrealized Tapes
- 1964: The Complete Last Recordings In Hilversum & Paris 1964
As sideman
With Ornette Coleman
With John Coltrane
- Olé Coltrane (1961)
- Africa/Brass (1961)
- Live! at the Village Vanguard (1961)
- Impressions (1963)
- Trane Whistle (Prestige, 1960)
With Phil Diaz
- The Latin Jazz Quintet (United Artists, 1961)
With Benny Golson
- Pop + Jazz = Swing (Audio Fidelity, 1961) – also released as Just Jazz!
With Chico Hamilton
- Chico Hamilton Quintet with Strings Attached (1958)
- The Original Ellington Suite (1958)
- Gongs East! (1958)
- That Hamilton Man (also released as Truth) (1959)
With Andrew Hill
- Point of Departure (1964)
With The Latin Jazz Quintet
- Caribe (Prestige) (1960)
With John Lewis
- The Sextet of Orchestra U.S.A. (1964)
- John Lewis Presents Jazz Abstractions (1960)
- Play Kurt Weill (1961)
- The Wonderful World Of Jazz (Track B2 “Afternoon In Paris – recorded Sept. 9, 1960 / released 1963)
With Abbey Lincoln
- Straight Ahead (Candid, 1961)
With Booker Little
- Out Front (1960)
With Ken McIntyre
- Looking Ahead (1960)
With Charles Mingus
- Mingus Revisited (aka Pre-Bird) (1960)
- Mingus at Antibes (1960)
- Charles Mingus Presents Charles Mingus (Candid, 1960)
- Mingus (Candid, 1960)
- The Complete 1960 Nat Hentoff Sessions (Candid, 1960)
- Mingus Mingus Mingus Mingus Mingus (1963)
- Town Hall Concert (1964)
- The Great Concert of Charles Mingus (1964)
- Revenge! (1964)
- Charles Mingus Sextet with Eric Dolphy: Cornell 1964 (1964)
- Complete Live In Amsterdam (1964)
- Complete Bremen Concert (1964)
- Astral Weeks (1964)
With Oliver Nelson
- Screamin’ the Blues (1960)
- The Blues and the Abstract Truth (1961)
- Straight Ahead (1961)
With Max Roach
- Percussion Bitter Sweet (1961)
With George Russell
- Ezz-thetics (1961)
With Mal Waldron
- The Quest (New Jazz, 1961)
With Ron Carter
- Where (New Jazz, 1961)
With Freddie Hubbard
With Ted Curson
- Plenty of Horn