Monteverdi: Scherzi Musicali (Turnabout, Club français du disque)
Flemish Musicians in Renaissance Italy (Turnabout)
A Renaissance Christmas (Turnabout, Advent)
A Medieval Christmas (Nonesuch, 1975)
Sing We Noel (Nonesuch, 1978)
Courts and Chapels of Renaissance France (Advent, Titanic)
German Music of the Middle Ages and Renaissance (Telefunken, Advent, Desmar)
The Roots of American Music (Advent)
Charpentier: Messe de Minuit and Sonate à 6 (Telefunken, Desmar, 1979)
Josquin: Missa Fortuna Desperata (Titanic)
Musique Judaeo-baroque (Harmonia Mundi, 1978)
Purcell: Dido and Aeneas (Harmonia Mundi, Sine Qua Non, 1980)
Certon: Mass and Chansons (Harmonia Mundi)
Machaut: Mass and Chansons (Harmonia Mundi 1983, Erato 1988)
Josquin: Missa Pange Lingua and motets (Harmonia Mundi)
Chants de l’Exil (Erato, 1980)
Nativitat: Mediterranean Christmas music (Ventadorn, 1979)
E viva Veniesia! A Venetian Festival (Erato 1983, Sine Qua Non 1984)
La Primavera: La nature dans la musique de la Renaissance (Erato, 1984)
A Renaissance Christmas (Nonesuch)
L’Homme armé: Music of war and peace (Erato, 1985)
Tristan & Iseult (Erato, 1987) — Grand Prix du Disque, 1989
New Britain: The Roots of American Folksong (Erato, 1988)
Noël, Noël: French Christmas music (Erato, 1987)
The Sacred Bridge (Erato, 1988)
Lo Gai Saber (Erato, 1990)
Jean Gilles: Requiem (Erato)
The American Vocalist: Spirituals and Folk Hymns, 1850-1870 (Erato, 1991)
A Baroque Christmas (Nonesuch, 1991)
Nueva España: Close Encounters in the New World, 1590-1690 (Erato, 1992)
An American Christmas (Erato, 1993)
Le Fou sur le pont (Erato, 1993)
With Joyful Voice (Nonesuch: box set of three Christmas recordings)
Le Roman de Fauvel (Erato, 1990)
Jean Gilles and others: Lamentations (Erato, 1994)
Music and Memory (compilation of Music Director Emeritus Joel Cohen’s work, Erato, 1995)
Simple Gifts: Shaker chants and spirituals (Erato, 1994)
John Dowland: Farewell Unkind (Erato, 1995)
Kurt Weill: Johnny Johnson (Erato, 1996)
Trav’ling Home (Erato, 1994)
Carmina Burana (Erato, 1996)
Douce Beauté: Pierre Guédron and the air de cour circa 1610 (Erato, 1997)
Liberty Tree: American Music, 1776-1859 (Erato)
Angels (Erato, 1996)
What Then is Love? An Elizabethan Songbook (Erato, 1997)
The Golden Harvest: More Shaker chants and spirituals (Glissando, 2000)
A Mediterranean Christmas (Warner Classics)
A Boston Camerata Christmas (Erato/Warner box set)
Treasures of Devotion (Music and Arts/Naxos, 2019)
Free America: Songs of Resistance and Rebellion (Harmonia Mundi, 2019)
Hodie Christus Natus Est: A Medieval Christmas (Harmonia Mundi, 2021)