| Year | Orchestra | Composer | Work (and soloists, if any) | Label |
| 1991 | London Symphony Orchestra | Adam | Music from "Giselle" | Sony |
| 1990 | London Symphony Orchestra, Ambrosian Singers | Beethoven | Late Choral Music | CBS Masterworks |
| 1986 | Orchestra of St. Luke's | Beethoven | Symphony No. 3 Contredanses for Orchestra, WoO 14 | CBS Masterworks |
| 2010 | San Francisco Symphony | Beethoven | Symphony No. 5 Piano Concerto No. 4 (Ax) | SFS Media |
| 1999 | English Chamber Orchestra | Beethoven | Symphony No. 6, "Pastorale" | Sony Classical |
| 1996 | London Symphony Orchestra | Bernstein | Arias and Barcarolles (von Stade, Hampson), Suite from A Quiet Place and Symphonic Dances from West Side Story. For details, see Arias and Barcarolles (Michael Tilson Thomas recording) | Deutsche Grammophon |
| 1993 | London Symphony Orchestra, London Voices | Bernstein | On the Town (Daly, von Stade, Lear, Laine, McLaughlin, Hampson, Garrison, Ollmann, Ramey) For details, see On the Town (Michael Tilson Thomas recording) | Deutsche Grammophon |
| 1991 | London Symphony Orchestra | Brahms | Serenade No. 1Tragic OvertureAcademic Festival Overture | Sony Classical |
| 1992 | London Symphony Orchestra | Brahms | Serenade No. 2 / HaydnVariations / HungarianDances – selections | Sony Classical |
| 2002 | | StravinskyCageReich | The Rite of Spring Three DancesFour Organs | Angel Records |
| 1996 | San Francisco Symphony | Copland | Concerto for Piano and OrchestraOrchestra VariationsShort SymphonySymphonic Ode (with Garrick Ohlsson) | RCA Victor Red Seal |
| 1972 | Boston Symphony Orchestra | Debussy | ImagesPrélude À L'Après-Midi D'Un Faune | Deutsche Grammophon |
| 1993 | London Symphony Orchestra and Chorus | Debussy | Le martyre de St. Sebastien (with McNair, Murray, Stutzman, Caron) | Sony Classical |
| 2007 | Boston Symphony Orchestra Chamber Players | Debussy | Sonata No. 1 for Cello and Piano (Eskin, Tilson Thomas) Sonata No. 2 for Flute, Viola and Harp (Dwyer, Fine, Hobson)Violin Sonata (Silverstein, Tilson Thomas) | Deutsche Grammophon |
| 1999 | New World Symphony | Feldman | Coptic Light (Cohen, Feinberg) | Argo |
| 1976 | Columbia Jazz Band,New York Philharmonic | Gershwin | Rhapsody in Blue (composer, piano roll)An American in Paris | Columbia |
| 1990 | Los Angeles Philharmonic Orchestra | Gershwin | Gershwin Live! (Vaughan, Tilson Thomas) | Sony Classical |
| 1984 | Los Angeles Philharmonic Orchestra | Gershwin | Rhapsody in Blue (Tilson Thomas)Second Rhapsody for Orchestra with Piano Preludes for Piano PromenadeUnpublished Piano Works | Columbia |
| 1970 | Boston Symphony Orchestra | IvesRugglesPiston | Three Places in New EnglandSun-treader | Deutsche Grammophon |
| 1991 | Chicago Symphony Orchestra | Ives | Symphonies Nos. 1 & 4 | Sony Classical |
| 2002 | San Francisco Symphony | Ives | An American Journey | RCA Victor Red Seal |
| 1990 | Chicago Symphony Orchestra and Chorus | Ives | Holiday SymphonyUnanswered Question (Herseth)Central Park in the Dark | Sony Classical |
| 1992 | London Symphony Orchestra and Chorus | Janáček | Glagolitic Mass (Benackova, Palmer, Lakes, Kotscherga)Sinfonietta | Sony Classical |
| 1974 | London Symphony Orchestra | Mahavishnu | Apocalypse (Mahavishnu Orchestra) | Sony Classical |
| 2004 | San Francisco Symphony | Mahler | Symphony No. 1 | SFS Media |
| 2004 | San Francisco Symphony and Chorus | Mahler | Symphony No. 2 | SFS Media |
| 2004 | San Francisco Symphony and Chorus,Pacific Boychoir,San Francisco Symphony Girls Chorus | Mahler | Symphony No. 3Kindertotenlieder (DeYoung) | SFS Media |
| 2004 | San Francisco Symphony | Mahler | Symphony No. 4 (Claycomb) | SFS Media |
| 2004 | San Francisco Symphony | Mahler | Symphony No. 5 | SFS Media |
| 2004 | San Francisco Symphony | Mahler | Symphony No. 6 | SFS Media |
| 2005 | San Francisco Symphony | Mahler | Symphony No. 7 | SFS Media |
| 2009 | San Francisco Symphony and Chorus, Pacific Boychoir, San Francisco Girls Chorus | Mahler | Symphony No. 8 | SFS Media |
| 2005 | San Francisco Symphony | Mahler | Symphony No. 9 | SFS Media |
| 2008 | San Francisco Symphony | Mahler | Das Klagende Lied (Shaguch, DeYoung, Moser, Lieferkus)Das Lied von der Erde (Skelton, Hampson) | RCA Red Seal |
| 1990 | London Symphony Orchestra and Chorus, South End Boys | Mahler | Symphony No. 3 Rückert Lieder (Baker) | Sony Classical |
| 1999 | London Symphony Orchestra | Mahler | Symphony No. 7 | RCA Victor Red Seal |
| 2010 | San Francisco Symphony | Mahler | Songs with Orchestra (Graham, Hampson) | SFS Media |
| 1998 | New World Symphony | New World Jazz | New World Jazz | RCA Victor Red Seal |
| 1997 | London Symphony Orchestra | Prokofiev | Symphonies Nos. 1 & 5 | Sony Classical |
| 2004 | San Francisco Symphony | Prokofiev | Romeo & Juliet | RCA Red Seal |
| 1991 | Hungarian State Orchestra | Puccini | Tosca (Marton, Carreras, Pons, Tajo) | Sony Classical |
| 1989 | London Symphony Orchestra | Ravel | Ma mère l'oyeBoleroPavane pour une infante défuntePièce en forme de HabañeraL'éventail de JeanneFanfare | Sony Classical |
| 1990 | Colorado Quartet, Brooklyn Philharmonic Orchestra | Reich | The Desert Music | Nonesuch |
| 1994 | London Symphony Orchestra | Reich | The Three movements | Nonesuch |
| 1980 | Buffalo Philharmonic | Ruggles | Complete Music of Carl Ruggles | Columbia |
| 1971 | Boston Symphony Orchestra | SchumanPiston | Violin Concerto (Paul Zukofsky)Symphony No. 2 | Deutsche Grammophon |
| 1986 | London Symphony Orchestra | Strauss, R. | Ein HeldenlebenTill Eulenspiegels Lustige Streiche | Columbia |
| 1972 | Boston Symphony Orchestra | Stravinsky | Le sacre du printempsLe roi des etoiles | Deutsche Grammophon |
| 1997 | London Symphony Orchestra | Stravinsky | Stravinsky in America | Sony Classical |