| Op. 4 | Adam and Eve (1961) for Piano |
| Op. 16 | Sonata for Flute and Cello (1962, rev. 1975) for Flute and Cello |
| Op. 18 | Sonata No. 1 for Violin and Piano (1963, rev. 2004) for Violin and Piano |
| Op. 19 | String Quartet No. 2 (1963, rev. 1993) for String Quartet |
| Op. 21 | Agnus Dei (1963) for SATB Chorus |
| Op. 22 | Psalm XXIII (1963) for Voice and Piano |
| Op. 25 | Piano Sonata No. 1 (1963) for Piano |
| Op. 26 | Woodwind Quintet (1964, rev. 1998) for Woodwind Quintet |
| Op. 28a | Benedictus (1964) for SATB Chorus |
| Op. 29a | Scherzo for Orchestra (1964) for Orchestra |
| Op. 30 | Piano Concerto No. 2 (1965) for Piano and Orchestra |
| Op. 31 | Fantasia quasi una Toccata (1965, rev. 1982) for Brass Octet and Four Percussionists |
| Op. 32 | String Quartet No. 3 (1965, rev. 1992) for String Quartet |
| Op. 34 | Missa Greensleeves (1967) for SATB Chorus |
| Op. 35 | Piano Quintet No. 1 (1967) for Piano and String Quartet |
| Op. 36 | Five Meditations (1967, rev. 1974/80) for English Horn, Harp, and Strings |
| Op. 37 | Nine Tagore Madrigals (1968) for SAQTB Voices |
| Op. 38 | Canzona sopra un tema di Monteverdi (1968) for Brass Nonet and Viola |
| Op. 39 | Concertino (1968, rev. 1988) for Harp, Harpsichord, Celesta, and Piano |
| Op. 40 | Six Pastoral Dances (1968) for Orchestra |
| Op. 41 | Sonata No. 1 for Cello and Piano (1968, rev. 1977) for Cello and Piano |
| Op. 44 | A Gentle Musicke (1969) for Flute and Strings |
| Op. 45 | Perchance to Dream (1969) for Orchestra |
| Op. 46 | Christmas Frescoes (1969, rev. 1996) for Piano and Five Percussionists |
| Op. 46a | Aria (1969/96) for Piano |
| Op. 47 | String Sextet: Nun komm’ der Heiden Heiland (1970, rev. 1997) for String Sextet (Two Violins, Two Violas, Two Cellos) |
| Op. 48 | Piano Sonata No. 2 (1970) for Piano |
| Op. 49 | And He Sent Forth a Dove (1971) for Piano |
| Op. 50 | Missa L’homme armé (1971) for SATB Chorus |
| Op. 51 | A My Lai Elegy (1971, rev. 1993) for Orchestra |
| Op. 52 | La Vie antériure (1971) for Male Voice, Three Trombones, Chimes, Gong, and String Quartet |
| Op. 53 | Wedding March (1971) for Piano |
| Op. 54 | Sonata for Oboe and Piano (1972) for Oboe and Piano |
| Op. 54a | Sonata No. 2 for Violin and Piano (1972) for Violin and Piano |
| Op. 55 | The Leaving Light (1972) for Voice and Piano |
| Op. 56 | String Quartet No. 4 (1972) for String Quartet |
| Op. 57 | Symphony No. 5, “Missa sine Cantoribus super Salve Regina” (1973) for Orchestra |
| Op. 58 | Three Elegiac Songs (1973) for Voice and Piano |
| Op. 59 | Requiem (1973) for Soloists, SATB Chorus, Orchestra |
| Op. 59a | To All, To Each (1973) for SATB Chorus |
| Op. 60 | Concerto Grosso No. 1 (1974) for Orchestra |
| Op. 61 | Musique de Clavecin (1974) for Harpsichord |
| Op. 62 | Missa In nomine (1974) for SATB Chorus |
| Op. 63 | Canzona Secundi Toni (1975) for Brass Choir (Three Trumpets, Three Horns, Three Trombones, and Tuba) |
| Op. 64 | Symphony No. 6 (1976) for Orchestra |
| Op. 65 | Five Ko-ans for Orchestra (1976) for Orchestra |
| Op. 66 | String Quartet No. 5 (1977) for String Quartet |
| Op. 67 | Responses, Hosanna, and Fugue (1977) for String Orchestra and Harp |
| Op. 68 | Nocturne (1978) for Orchestra |
| Op. 69 | Piano Sonata No. 3, “Sonata Eterea” (1978) for Piano |
| Op. 70 | Brass Quintet (1978) for Brass Quintet |
| Op. 71 | Sonata for Horn and Piano (1979) for Horn and Piano |
| Op. 72 | Magnificat (1979) for SATB Chorus, Two Trumpets, and Two Trombones |
| Op. 73 | Nightstone (1979) for Voice and Piano |
| Op. 74 | Concerto Grosso No. 2 (1979) for Orchestra |
| Op. 75 | Consort Music (1980) for Five Violas da Gamba |
| Op. 75a | Consort Music (1980) for Orchestra |
| Op. 76 | Prelude and Fugue (1980) for Six Percussionists |
| Op. 77 | Minstrel to an Unquiet Lady (1982) for Tenor and Piano |
| Op. 78 | Symphony No. 7, “The Tragedy of Queen Jane” (1982) for Orchestra |
| Op. 79 | Of Numbers and of Bells (1983) for Two Pianos |
| Op. 80 | Let Them Praise (1984) for Two-Part Chorus (Treble, Men's, or Mixed), Organ, and Handbells/Chimes |
| Op. 81 | The Chronicle of Nine: The Tragedy of Queen Jane (1984) for Soprano, Two Altos, Four Tenors, Two Baritones, Bass, SATB Chorus, Orchestra (Opera in Three Acts) |
| Op. 82 | From the Diaries of Adam Czerniakow (1986) for Narrator and Orchestra |
| Op. 83 | Sonatine d’Amour (1987) for Harpsichord |
| Op. 84 | Symphony No. 8, “Trinity” (1988) for Band |
| Op. 85 | A Plaintive Harmony (1988) for Horn |
| Op. 86 | Besos sin cuento (1989) for Alto, Flute, Viola, and Harp |
| Op. 87 | Transformations (1989) for Trumpet, Piano, and Strings |
| Op. 88 | Lovely Joan: Rhapsody on an English Folk Song (1990) for Band |
| Op. 89 | Sonata No. 2 for Cello and Piano, “La Divina Commedia” (1990) for Cello and Piano |
| Op. 90 | Songs of Lightness and Angels (1990) for Soprano, Horn, and Piano |
| Op. 91 | De Profundis (1991) for Band |
| Op. 92 | A Psalm of Mercy (1991) for SATB Soloists, SATB Chorus, and Keyboard |
| Op. 93 | Gematria (1991) for Orchestra |
| Op. 93a | Gematria Prologue (1991/2001) for Trumpet and Organ |
| Op. 94 | A Duet for Violas (1991) for Two Violas |
| Op. 94a | A Duet for Cellos (1991) for Two Cellos |
| Op. 95 | A Sephardic Rhapsody (1992) for Orchestra |
| Op. 96 | Poseidon (1993) for Voice and Piano |
| Op. 97 | The Parable of the Law (1993) for Baritone and Orchestra |
| Op. 98 | Dances of Initiation (1993) for Band |
| Op. 99 | Etz Chaim (1993) for Piano |
| Op. 100 | Eclipse (1994) for Band |
| Op. 101 | Danses à la mode (1994) for Cello |
| Op. 101a | Danses à la mode (1994) for Violin |
| Op. 102 | Bontsche Schweig (1994) for Two Sopranos, Alto, Two Tenors, Baritone, Bass, and Chamber Orchestra (Opera in One Act) |
| Op. 102a | Bontsche Dances (1994) for Piano |
| Op. 103 | Piano Quintet No. 2 (1995) for Piano and String Quartet |
| Op. 104 | RAGA! (1995) for Band |
| Op. 105 | Variations on a Theme by Frank Martin (1996) for Orchestra |
| Op. 106 | Sonata for Trombone and Piano (1996) for Trombone and Piano |
| Op. 107 | Concerto for Two Trumpets, Timpani, and Strings (1997) for Two Trumpets, Timpani, and Strings |
| Op. 108 | Of Songs and Sonnets (1997) for Countertenor (or Mezzo-Soprano) and Harpsichord |
| Op. 109 | Tempus Perfectum (1998) for Orchestra |
| Op. 110 | Serpentine (1999) for Clarinet and Piano |
| Op. 111 | To the Keen Stars (1999) for Voice and Piano |
| Op. 112 | A Millennium Overture (1999) for Orchestra |
| Op. 113 | Concerto for Harpsichord and Strings (2000) for Harpsichord and Strings |
| Op. 114 | 3^7 (2000) for Harp |
| Op. 115 | Clausulae for Trombones (2001) for Three Trombones |
| Op. 116 | Strictly Personals (2001) for Soprano, Baritone, and String Quartet (or Piano) |
| Op. 117 | Three Northern Sketches (2003) for Band |
| Op. 118 | String Quartet No. 6 (2004) for String Quartet |
| Op. 119 | Now Cometh the Redeemer (2005) for Band |
| Op. 120 | Five (2005) for Voice and Piano |
| Op. 121 | Sonata for Bassoon and Piano (2006) for Bassoon and Piano |
| Op. 122 | Unraveling Dances (2007) for Orchestra |
| Op. 123 | Spinoza (2011) for Soprano, Mezzo-Soprano (or Countertenor), Two Tenors, Three Baritones, Chamber Orchestra (Opera in One Act) |
| Op. 124 | Minyan (2013) for Viola and Guitar |
| Op. [1] | Chromatic Fantasy (by Jan Pieterszoon Sweelinck) (1987) for Band |
| Op. [2] | Open School Night [stage play] (2004) |
| Op. [3] | An Analytical Survey of the Music of Alan Hovhaness [dissertation] (1972) |
| Op. [4] | A New Tool for Harmonic Analysis: Valence Theory [article] (1979?) |