| 1974 | Concert Royaux, Nouveaux Concerts, L'Apothéose de Corelli, L'Apothéose de Lully, Sonatas "La Superbe", "La Steinquerque", "La Sultane" | François Couperin; Sigiswald Kuijken, Wieland Kuijken& Bart Kuijken | | 1 |
| 1977 | Complete Wind Music | Jacques Martin Hotteterre; Brüggen, B. & W. Kuijken, Haynes, Leonhardt | | 1 |
| 1979 | Six Trios op. 38 for Transverse Flute, Violin and Violoncello | Joseph Haydn; Barthold Kuijken, Sigiswald Kuijken, Wieland Kuijken | | 2 |
| 1982 | The Flute Quartets | Wolfgang Amadeus Mozart; Barthold Kuijken, Sigiswald Kuijken, Lucy van Dael, Wieland Kuijken | | 2 |
| 1984 | The Complete Flute Sonatas | Jean‐Marie Leclair; Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 1985 | Musical Offering | J.S. Bach Gustav Leonhardt, Conductor & Harpsichordist Barthold Kuijken * Sigiswald Kuijken * Wieland Kuijken * Robert Kohnen | | 1 |
| 1986 | Six Trios For Transverse Flute, Violin And Violoncello - Volume II | Joseph Haydn; Barthold Kuijken, Sigiswald Kuijken, Wieland Kuijken | | 1 |
| 1987 | Concerts Royaux | Couperin; Sigiswald Kuijken, Wieland Kuijken, Barthold Kuijken | | 1 |
| 1989 | Concerts Royaux 1-4 | Couperin; Sigiswald Kuijken, Bart Kuijken, Wieland Kuijken | | 1 |
| 1991 | German Chamber Music | Barthold Kuijken, Sigiswald Kuijken, Wieland Kuijken & Robert Kohnen | | 1 |
| 1991 | Flute Sonatas | George Frideric Händel; Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 1991 | Italian Flute Sonatas | Corelli, Geminiani, Veracini, Locatelli, Albinoni, Vivaldi, Platti; Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 1992 | Flute Concertos | C. Stamitz, J. Stamitz, Richter, Haydn, Gluck; Barthold Kuijken, Tafelmusik, Jeanne Lamon | | 1 |
| 1993 | Troisiéme Livre de Piéces de Clavecin - 1722 | François Couperin;Robert Kohnen & Barthold Kuijken | | 1 |
| 1994 | "Sonate Metodiche" 1728 / 1732 | Georg Philipp Telemann; Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 1995 | Musicalisches Opfer / Musical Offering BWV 1079 | Barthold Kuijken, Sigiswald Kuijken, Wieland Kuijken & Robert Kohnen | | 1 |
| 1997 | Musikalisches Opfer, BWV 1079 | J. S. Bach; Barthold Kuijken, Robert Kohnen, Gustav Leonhardt | | 3 |
| 1997 | Paris Quartets 1-12 | Georg Philipp Telemann; Barthold Kuijken, Sigiswald Kuijken, Wieland Kuijken, Gustav Leonhardt | | 1 |
| 1998 | Nouveaux concerts from Les Goûts réunis | François Couperin; Kuijken, Rubinlicht, Haynes, Kohnen | | 1 |
| 2000 | Six Duets For Two Flutes | Wilhelm Friedemann Bach; Barthold Kuijken, Marc Hantai | | 1 |
| 2002 | Concerti per flauto traversiere | Vivaldi, Barthold Kuijken, Academia Montis Regalis | | 3 |
| 2002 | Flute Sonatas | J. S. Bach; Barthold Kuijken, Ewald Demeyere | | 1 |
| 2003 | Concerts Royaux | François Couperin; Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 2004 | Flute Quartets | François Devienne; Barthold Kuijken, Ryo Terakado, Sara Kuijken, Wieland Kuijken | | 1 |
| 2005 | Twelve Trios for Transverse Flute, Violin & Violoncello | Joseph Haydn; Barthold Kuijken, Wieland Kuijken, Sigiswald Kuijken | | 1 |
| 2007 | The Sonatas for Flute and Basso Continuo | C.P.E. Bach; Barthold Kuijken, Ewald Demeyere | | 1 |
| 2007 | French and Italian Flute Music of the 18th Century | Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| 2008 | Bach Sons - Flute Sonatas | Barthold Kuijken & Ewald Demeyere | | 1 |
| 2012 | Cantata da Camera | Nicola Porpora; Antonio Caldara; George Frideric Handel; René Jacobs, Barthold Kuijken, Sigiswald Kuijken, Anner Bylsma, Gustav Leonhardt | | 1 |
| 2012 | Complete Flute Sonatas | C.P.E. Bach; Barthold Kuijken, Bob van Asperen | | 1 |
| 2018 | The Lully Effect | Lully, Telemann, Rameau; Indianapolis Baroque Orchestra, Barthold Kuijken | | 2 |
| 2018 | The Versailles Revolution | Jean‐Baptiste Lully, Georg Muffat, Marin Marais; Indianapolis Baroque Orchestra, Barthold Kuijken | | 2 |
| 2019 | The Grand Mogul: Virtuosic Baroque Flute Concertos | Blavet, Leclair, Pergolesi, Telemann, Vivaldi; Barthold Kuijken, Indianapolis Baroque Orchestra | | 2 |
| 2020 | The Colorful Telemann | Telemann; Indianapolis Baroque Orchestra, Barthold Kuijken | | 1 |
| — | French Flute Music of the Eighteenth Century | Barthold Kuijken, Wieland Kuijken, Robert Kohnen | | 1 |
| — | Solo pour la flute traversiere | Barthold Kuijken | | 1 |
| — | The twelve Fantasias for Transverse Flute without Bass | Georg Philipp Telemann; Barthold Kuijken | | 2 |
| — | W.A. Mozart: Flötenkonzerte K 313/314; Andante K 315 | Wolfgang Amadeus Mozart, La Petite Bande, Sigiswald Kuijken & Barthold Kuijken | | 1 |
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