| 1998 |
Cantatas, Volume 8 |
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| 1998 |
Weihnachts-Oratorium |
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| 1998 |
Geistliche Chormusik op. 11 |
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| 1998 |
Cantatas, Volume 9 |
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| 1999 |
Johannes-Passion, BWV 245 |
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| 1999 |
Magnificat |
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| 1999 |
Cantatas, Volume 10 |
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| 1999 |
Inventionen & Sinfonien |
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| 1999 |
Cantatas, Volume 11 |
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| 1999 |
Matthäus-Passion, BWV 244 |
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| 2000 |
Cantatas, Volume 12 |
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| 2000 |
Concertos, Volume 1 |
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| 2000 |
Fantasias & Fugues |
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| 2000 |
Cantatas, Volume 13 |
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| 2000 |
Clavier-übung III |
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| 2001 |
Vespro della Beata Vergine / Missa in illo tempore |
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| 2001 |
Concertos, Volume 2: Brandenburg Concertos, BWV 1046-1051 |
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| 2001 |
Cantatas, Volume 14 |
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| 2001 |
Brandenburg Concertos |
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| 2001 |
Cantatas, Volume 15 |
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| 2001 |
Cantatas, Volume 16 |
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| 2002 |
Cantatas, Volume 17 |
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| 2002 |
Cantatas, Volume 18 |
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| 2002 |
Cantatas, Volume 19 |
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| 2002 |
Partitas for Harpsichord |
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| 2002 |
Cantatas, Volume 20 |
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| 2003 |
Cantatas, Volume 21 |
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| 2003 |
French Suites |
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| 2003 |
Cantatas, Volume 22 |
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| 2003 |
Cantatas, Volume 23 |
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| 2004 |
Cantatas |
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| 2004 |
Cantatas, Volume 24 |
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| 2004 |
Cantatas, Volume 25 |
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| 2004 |
Secular Cantatas: O holder Tag BWV 210 / Coffee Cantata BWV 211 |
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| 2004 |
Cantatas, Volume 26 |
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| 2005 |
Early Italian Chamber Music |
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| 2005 |
Cantatas, Volume 27 |
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| 2005 |
Messiah Highlights |
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| 2005 |
Cantatas, Volume 28 |
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| 2005 |
Ouvertures (Orchestral Suites) (Orchestra of the Bach Collegium Japan feat. conductor: Masaaki Suzuki) |
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| 2005 |
Cantatas, Vol. 29 (BWV 2, 3, 38, 135) |
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| 2005 |
Easter Oratorio / Ascension Oratorio |
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| 2006 |
Cantatas, Volume 30 |
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| 2006 |
Italian Concerto / French Overture / Sonata in D minor |
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| 2006 |
Cantatas, Vol. 31 (BWV 91, 101, 121, 133) |
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| 2006 |
Cantatas, Volume 32 |
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| 2006 |
Psalms From Geneva |
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| 2006 |
Cantatas, Volume 33 |
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| 2007 |
Cantatas, Volume 34 |
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| 2007 |
Cantatas, Volume 35 |
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| 2007 |
Cantatas, Volume 36 |
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| 2007 |
Mass in B minor |
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| 2007 |
Cantatas, Volume 37 |
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| 2008 |
Cantatas, Volume 38 |
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| 2008 |
Cantatas, Vol. 39 (BWV 68, 175, 28, 183, 85) |
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| 2008 |
Cantatas, Volume 40 |
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| 2008 |
Cantatas, Volume 41 |
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| 2008 |
Das Wohltemperierte Klavier II |
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| 2009 |
Cantatas, Volume 42 |
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| 2009 |
Cantatas, Volume 43 |
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| 2009 |
Cantatas, Volume 44 |
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| 2009 |
Brandenburg Concertos Nos. 1-6 / Orchestral Suites Nos. 1-4 |
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| 2009 |
Cantatas, Volume 45 |
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| 2010 |
Motets |
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| 2010 |
Masaaki Suzuki plays Buxtehude |
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| 2010 |
Cantatas, Volume 46 |
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| 2010 |
A Choral Year With Bach |
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| 2010 |
Cantatas, Volume 47 |
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| 2011 |
Cantatas, Volume 48 |
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| 2011 |
Cantatas, Volume 49 |
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| 2011 |
Cantatas, Volume 50 |
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| 2012 |
Secular Cantatas, Vol. 2 |
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| 2012 |
Cantatas, Volume 51: Nun danket alle Gott. Cantatas 120a, 157, 192, 195 |
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| 2012 |
Cantatas, Volume 52 |
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| 2013 |
Cantatas, Volume 53 |
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| 2013 |
Secular Cantatas, Volume 3 |
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| 2013 |
Cantatas, Volume 54 |
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| 2013 |
Cantatas, Volume 55 |
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| 2014 |
Requiem |
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| 2014 |
Secular Cantatas, Volume 4: Academic Cantatas |
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| 2014 |
Concertos for 2 Harpsichords |
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| 2015 |
Lutheran Masses II |
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| 2015 |
Birthday Cantatas |
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| 2015 |
Lutheran Masses I |
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| 2015 |
Masaaki Suzuki plays Bach Organ Works |
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| 2016 |
Secular Cantatas, Volume 6: Trauerode |
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| 2016 |
Pulcinella Suite / Apollon Musagète / Concerto in D for Strings |
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| 2016 |
Secular Cantatas, Vol. 7: Peasant Cantata |
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| 2016 |
Great Mass in C minor / Exsultate, jubilate |
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| 2017 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 2 |
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| 2017 |
Secular Cantatas, Volume 8: Celebratory Cantatas |
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| 2017 |
Musikalisches Opfer |
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| 2017 |
Secular Cantatas, Volume 9: The Contest between Phoebus and Pan |
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| 2018 |
Missa solemnis |
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| 2018 |
Secular Cantatas, Volume 10: Cantatas of contentment |
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| 2018 |
Verbum caro factum est - A Christmas Greeting |
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| 2019 |
English Suites |
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| 2019 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 3 |
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| 2019 |
Symphony no. 9 |
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| 2020 |
St. Matthew Passion |
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| 2020 |
Toccatas |
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| 2020 |
St. John Passion (The Köln Recording) |
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| 2022 |
Cantatas and Organ Works, Vol. 1 |
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| 2023 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 4: orgelbüchlein (I) |
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| 2024 |
Die Kunst der Fuge, BWV 1080 |
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| 2024 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 5 |
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| 2024 |
Symphony no. 4 in E minor, op. 98 (Version for Piano 4 Hands) |
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| 2024 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 6 |
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| 2025 |
Masaaki Suzuki Plays Bach Organ Works, Vol. 7 |
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| 2026 |
Symphony no. 2, op. 52, "Lobgesang" |
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Cantatas, Vol. 1 (BWV 4, 150, 196)
Cantatas, Volume 2
Cantatas, Volume 3
Cantatas, Volume 4
Das Wohltemperierte Klavier, Book I
Messiah
Cantatas, Volume 5
Complete Keyboard Works, Volume 2: Goldberg Variations
Membra Jesu Nostri
Cantatas, Volume 6
Cantatas, Volume 7