As leader edit

• Trials of the Argo (Lumina, 1981)
• Portal (Lumina, 1983)
• Trespass (Lumina, 1986)
• Overlays (Moers, 1991)
• Opposites Attract with Paul Dresher (New World, 1991)
• Power Lines (New World, 1995)
• Real and Imagined Time (Moers, 1995)
• Amulet with Sainkho (Leo, 1996)
• Monkey Puzzle with Evan Parker (Leo, 1997)
• Port of Entry (Intuition, 1998)
• Ghost Stories (Tzadik, 2000)
• Tools of The Trade with Denman Maroney, (CIMP, 2001)
• Intervals (Animul, 2002)
• Decisive Action with Satoh Masahiko (BAJ, 2004)
• En Passant with Peter A. Schmid (Creative Works, 2004)
• Harbinger (Animul, 2004)
• Falling into Place with Slava Ganelin (Auris Media, 2006)
• El Nino with Matthias Ziegler, Peter A. Schmid (Creative Works, 2006)
• Live at Roulette with Evan Parker (Animul, 2007)
• The Fell Clutch with Tony Buck, Stomu Takeishi (Animul, 2007)
• Inner Diaspora (Tzadik, 2007)
• While You Were Out with Catherine Jauniaux, Barre Phillips (Kadima Collective, 2009)
• Free Zone Appleby 2007 with Evan Parker, Paolo Angeli (psi, 2009)
• Live at DOM with Vladimir Volkov (Dom, 2010)
• Quintet for Clarinet and Strings (Tzadik, 2010)
• Ryu Nashi/No School-New Music for Shakuhachi (Tzadik, 2010)
• World of Odd Harmonics (Tzadik, 2012)
• In Cahoots with Mark Feldman, Sylvie Courvoisier, (Clean Feed, 2016)
• Strings 2 with Perelman/Maneri/Roberts (Leo, 2018)

With New Winds

• The Cliff (Sound Aspects, 1989)
• Traction (Sound Aspects, 1991)
• Digging It Harder from Afar (Les Disques Victo, 1995)
• Potion (Les Disques Victo, 1998)

With Semantics

• Semantics (Review, 1986)
• Bone of Contention (SST, 1987)

As sideman edit

With Anthony Braxton

• Creative Orchestra (Köln) 1978 (hatART, 1995)
• Trillium R (Braxton House, 1999)
• Orchestra (Paris) 1978 (Braxton Bootleg, 2011)

With Robert Dick

• Venturi Shadows (OODiscs, 1991)
• Worlds of If (Leo, 1995)

With Kip Hanrahan

• Desire Develops an Edge (American Clave, 1983)
• Vertical's Currency (American Clave, 1985)

With Denman Maroney

• Fluxations (New World, 2003)
• Gaga (Nuscope, 2008)
• Udentity (Clean Feed, 2009)

With Steve Nieve

• Mumu (Silvertone, 2001)
• Welcome to the Voice (Deutsche Grammophon, 2007)

With Evan Parker

• The Moment's Energy (ECM, 2009)
• Hasselt (psi, 2012)
• Seven ElectroAcoustic Septet (Les Disques Victo, 2014)

With Marc Ribot

• Music from the Performance Inasmuch As Life Is Borrowed (Ultima Vez, 2001)
• Scelsi Morning (Tzadik, 2003)
• Soundtracks Volume 2 (Tzadik, 2003)

With Adam Rudolph

• Dream Garden (Justin Time, 2008)
• Can You Imagine...The Sound of a Dream (Meta, 2011)

With Steve Swell

• Flurries Warm and Clear (CIMP, 2000)
• Kanreki: Reflection & Renewal (Not Two, 2015)

With John Zorn

• The Big Gundown (Nonesuch, 1986)
• Music Romance Volume III: The Gift (Tzadik, 2001)
• Dictée/Liber Novus (Tzadik, 2010)

With others

• Anthony Coleman, Lapidation (New World, 2008)
• Samm Bennett, The Big Off (Factory Outlet, 1993)
• Elvis Costello, The Juliet Letters (Rhino, 2006)
• Marty Ehrlich, The Long View (Enja, 2002)
• Nicolas Collins, 100 of The World's Most Beautiful Melodies (Trace Elements, 1989)
• Heiner Goebbels, Heiner Mueller, Der Mann Im Fahrstuhl (ECM, 1988)
• Phil Haynes Herb Robertson 5tet, Brooklyn-Berlin (CIMP, 2000)
• Jason Hwang, Unfolding Stone (Sound Aspects, 1990)
• Sato Michihiro, Rodan (hat ART, 1989)
• Marisa Monte, Green, Blue, Yellow, Rose and Charcoal (Metro Blue, 1994)
• Sainkho Namtchylak, Stepmother City (Ponderosa Music & Art, 2000)
• Roy Nathanson, Fire at Keaton's Bar & Grill (Six Degrees, 2000)
• Bob Ostertag, Bob Ostertag Plays the Serge 1978–1983 (Analogue Motions Studio, 2014)
• Bobby Previte, The 23 Constellations of Joan Miro (Tzadik, 2001)
• Liu Sola, Blues in the East (Axiom, 1994)
• Elliott Sharp, Radiolaria (Zoar, 2001)
• Daniel Zamir, Children of Israel (Tzadik, 2002)

• Official site
• Allmusic entry
• Interview with Ned Rothenberg by Sasha Burov (April 23, 2004) from Paris Transatlantic magazine
• Video interview by Derk Richardson for radiOM