| 1982 | Cantate di Natale | Zelenka, Fux, Jacobi, Schmelzer; Peter Schreier, Capella Sagittariana, Dietrich Knothe | | 1 |
| 1985 | Requiem in C minor | Jan Dismas Zelenka | | 1 |
| 1986 | Triosonaten, Volume 1 (oboe: Burkhard Glaetzner) | Jan Dismas Zelenka | | 1 |
| 1986 | Triosonaten, Volume 2 (oboe: Burkhard Glaetzner) | Jan Dismas Zelenka | | 1 |
| 1990 | Missa Dei Filii / Litaniae Lauretanae | Jan Dismas Zelenka; Tafelmusik, Kammerchor Stuttgart, Frieder Bernius | | 2 |
| 1990 | Lamentationes Jeremiae Prophetae: Lamentationen zur Karwoche | Jan Dismas Zelenka | | 1 |
| 1991 | Lamentations | Zelenka; Michael Chance, Michael George, John Mark Ainsley, Chandos Baroque Players | | 2 |
| 1993 | Sonates pour Deux Hautbois et Basson | Zelenka; Ensemble Zefiro | | 1 |
| 1993 | Trio Sonatas 1-3 | Jan Dismas Zelenka; Jana Brožková, Vojtěch Jouza, Jan Jouza, Jaroslav Kubita, Václav Hoskovec, František X. Thuri | | 1 |
| 1995 | Six Trio Sonatas For Oboe, Violin and Continuo | Jan Dismas Zelenka; Soloists of the Chamber Orchestra of Europe, Douglas Boyd, Rachel Frost, Matthew Wilkie, Marieke Blankestijn, Enno Senft, Ursula Dütschler | | 1 |
| 1995 | Sonates I, III, IV pour Deux Hautbois et Basson | Zelenka; Ensemble Zefiro | | 1 |
| 1995 | Trio Sonatas, ZWV 181 | Jan Dismas Zelenka; Ars Instrumentalis Pragensis | | 1 |
| 1996 | Miserere: Sacred Choral Pieces of the Dresden Baroque | Jan Dismas Zelenka, Johann Adolf Hasse, Johann David Heinichen, Gottfried August Homilius; Rheinische Kantorei, Das Kleine Konzert, Hermann Max | | 1 |
| 1997 | Complete Orchestral Works 1 | Jan Dismas Zelenka; Das Neu-Eröffnete Orchestre, Jürgen Sonnentheil | | 1 |
| 1998 | Musik aus der Dresdner Hofkirche - Missa Omnium Sanctorum | Jan Dismas Zelenka; Kammerchor Stuttgart, Barockorchester Stuttgart, Frieder Bernius | | 1 |
| 1998 | Missa Circumcisionis Domini Nostri Jesu Christi | Jan Dismas Zelenka | | 1 |
| 1999 | Trio Sonatas | Zelenka | | 1 |
| 1999 | Magnificat | Johann Kuhnau, Jan Dismas Zelenka, Johann Sebastian Bach; Bach Collegium Japan, Masaaki Suzuki | | 1 |
| 1999 | Complete Orchestral Works 2 | Jan Dismas Zelenka; Das Neu-Eröffnete Orchestre, Jürgen Sonnentheil | | 1 |
| 1999 | Responsoria pro Hebdomada Sancta | Jan Dismas Zelenka; Lumen Valo | | 1 |
| 2000 | Complete Orchestral Works 3 | Jan Dismas Zelenka; Das Neu-Eröffnete Orchestre, Jürgen Sonnentheil | | 2 |
| 2000 | Responsoria (Lumen Valo) | Jan Dismas Zelenka | | 1 |
| 2000 | De Profundis, Miserere & Requiem | Jan Dismas Zelenka | | 1 |
| 2000 | Office des Ténèbres du Vendredi Saint | Jan Dismas Zelenka; Paul Colléaux | | 1 |
| 2002 | The Solists of the Virtuosi Saxoniae | Georg Philipp Telemann, Johann Heinrich Schmelzer, Francesco Onofrio Manfredini, Jan Dismas Zelenka, Johann Joachim Quantz; Virtuosi Saxoniae, Ludwig Güttler | | 1 |
| 2002 | Sub olea pacis et palma virtutis | Jan Dismas Zelenka; Musica Florea, Musica Aeterna, Ensemble PhilidOr, Boni Pueri, Marek Štryncl | | 1 |
| 2003 | Sacred Music by Jan Dismas Zelenka | Jan Dismas Zelenka; Sampson, Outram, Blaze, Gilchrist, George, Harvey, Choir of the King’s Consort, The King’s Consort, Robert King | | 2 |
| 2007 | Missa Purificationis Beatae Virginis Mariae / Litaniae Lauretanae "Consolatrix Afflictorum" | Jan Dismas Zelenka; Ensemble Inégal, Adam Viktora | | 1 |
| 2008 | Missa Votiva, ZWV 18 | Zelenka; Collegium 1704, Collegium Vocale 1704, Václav Luks | | 3 |
| 2009 | I penitenti al sepolchro del redentore | Zelenka; Collegium 1704, Collegium Vocale 1704, Mariana Rewerski, Eric Stoklossa, Tobias Berndt, Václav Luks | | 3 |
| 2009 | Lotti, Zelenka, Bach | Antonio Lotti, Jan Dismas Zelenka, Johann Sebastian Bach; Thomas Hengelbrock, Balthasar-Neumann-Chor, Balthasar-Neumann-Ensemble | | 1 |
| 2010 | Missa votiva | Jan Dismas Zelenka; Kammerchor Stuttgart, Barockorchester Stuttgart, Frieder Bernius | | 2 |
| 2010 | Concertos | Jan Dismas Zelenka, Johann Georg Pisendel; Freiburger Barockorchester | | 1 |
| 2010 | Officium defunctorum ZWV 47 / Requiem in D ZWV 46 | Zelenka; Collegium 1704, Collegium Vocale 1704, Václav Luks | | 1 |
| 2010 | Zelenka | Jan Dismas Zelenka ; Pasticcio Barocco | | 1 |
| 2012 | Zelenka: Missa Nativitatis Domini, Magnificat | Jan Dismas Zelenka; Musica Florea, Marek Štryncl | | 1 |
| 2012 | Solo Motets | Zelenka; Alex Potter, Capriccio Barockorchester | | 1 |
| 2014 | František Ignác Tůma: Stabat Mater / Jan Dismas Zelenka: Santus / Agnus Dei ZWV 34 & 36 / Sub Tuum Præsidium ZWV 157 | František Ignác Tůma; Jan Dismas Zelenka; Collegium 1704, Václav Luks | | 1 |
| 2014 | Music from Eighteenth-century Prague | Jan Dismas Zelenka & František Ignác Tůma | | 1 |
| 2015 | Psalmi vespertini I | Jan Dismas Zelenka, Ensemble Inégal, Prague Baroque Soloists & Adam Viktora | | 1 |
| 2016 | Missa Divi Xaverri, ZWV 12 / Litaniae des Sancto Xaverio, ZWV 156 | Jan Dismas Zelenka; Václav Luks, Collegium Vocale 1704, Collegium 1704 | | 1 |
| 2017 | Sonatas, ZWV 181 | Jan Dismas Zelenka; Collegium 1704 | | 1 |
| 2017 | Zelenka | Zelenka;Pasticcio Barocco,Orchestre de Chambre d'Auvergne | | 1 |
| 2018 | Jan Dismas Zelenka: Trio Sonatas ZWV 181 | Jan Dismas Zelenka; Ensemble Berlin Prag | | 1 |
| 2021 | Missa Sancti Spiritus ZWV 4, Litanie di Vergine Maria ZWV 149 | Jan Dismas Zelenka; Ensemble Inégal / Adam Viktora | | 1 |
| 2022 | Grand Tour a Venezia | Heinichen, Lotti, Pisendel, Veracini, Vivaldi, Zelenka; Zefiro, Alfredo Bernardini | | 1 |
| — | Die Orchesterwerke = The Orchestral Works | Jan Dismas Zelenka / Camerata Bern | | 1 |
| — | Immisit Dominus pestilentiam, ZWV 58 / Attendite et videte ZWV 59 / Deus Dux fortissime ZWV 60 | Jan Dismas Zelenka; Collegium Marianum, Jana Semerádová | | 1 |
| — | Il Diamante | Jan Dismas Zelenka;Ensemble Inégal, Prague Baroque Soloists, Adam Viktora | | 1 |
| — | Il Serpente di Bronzo | Jan Dismas Zelenka; Ensemble Inégal, Adam Viktora | | 1 |
| — | Missa Sancti Josephi, ZWV 14 / Litaniae Xaverianae, ZWV 155 | Jan Dismas Zelenka; Ensemble Inégal, Prague Baroque Soloists, Adam Viktora | | 1 |
| — | Missa in D / Responsoria | Jan Dismas Zelenka; Pražský filharmonický sbor, Česká filharmonie, Jiří Bělohlávek | | 1 |
| — | Magnificat | Jan Dismas Zelenka | | 1 |
| — | Missa Paschalis / Litaniae Omnium Sanctorum | Jan Dismas Zelenka | | 1 |
| — | Missa Omnium Sanctorum ZWV 21 / Christe Eleison ZWV 29 / Barbara Dira Effera ZWV 164 | Jan Dismas Zelenka; Ensemble Inégal, Prague Baroque Soloists, Adam Viktora | | 1 |
| — | Missa Dei Patris / Confitebor Tibi Domine / Laudate Pueri | Jan Dismas Zelenka; Virtuosi Saxoniae, Ludwig Güttler | | 1 |
| — | Psalmi | Jan Dismas Zelenka | | 1 |
| — | Sonatas | Jan Dismas Zelenka; Marsyas, Monica Huggett | | 1 |
| — | Virtuouso Saxoniae, Ludwig Güttler | Johann Friedrich Fasch, Alessandro Scarlatti, Antonio Vivaldi, Johannes Matthias Sperger, Johann Georg Pisendel, Jan Dismas Zelenka; Ludwig Güttler, Virtuosi Saxoniae | | 1 |
