- DELECTVS SACRARVM CANTIONVM A II. III. IV. V. Vocibus, cum adjunctis Instrumentis. OPVS PRIMVM. Auctore JOHANNE CASPARO KERLL, München 1669 (Johann Jäcklin)
- MODVLATIO ORGANICA SVPER MAGNIFICAT OCTO ECCLESIASTICIS TONIS RESPONDENS. A IOAN:CASPARO KERLL. Ex omnifario Artificii Musici Genere concinnata, München 1686 (Michael Wening)
- Hoc Opus, Hic Labor. MISSAE SEX A IV. V. VI. Vocibus, cum Instrumentis concertantibus, & vocibus in Ripieno, Adjunctâ unâ pro Defunctis cum seq:[uentia] Dies irae CONSECRATAE LEOPOLDO I. IMPERATORI AVCTORE JOANNE CASPARO KERLL, München 1686 (Johannes Jäcklin)
- 1.Missa non sine quare
- 2.Missa Patientiae & spei
- 3.Missa SS. Innocentium
- 4.Missa Corona Virginum in trino & uno
- 5.Missa in fletu solatium
- 6.Missa Renovationis
- 7.Missa pro Defunctis
Handschriftlich überlieferte Werke:
- Missa Nigra
- Missa Superba
- Missa cuius Toni
- Missa Quasi modo Genita
- Missa a 3 Chori
Offertories:
- 1.Angelorum esca
- 2.Exsultent justi
- 3.Justus ut palma
- 4.Quemadmodum desiderat cervus
- 5.Stetit Angelus
- 6.Tota pulchra es Maria
- 7.Triumphate sidera
- Magnificat in A (vierstimmig)
- Magnificat (sechsstimmig)
- Laudate pueri
- Ricercata a 4 in A for keyboard instrument – published in Athanasius Kircher's Musurgia universalis (Rome, 1650)
- 16 sacred works on Latin texts, 3 on German texts
- Pia et fortis mulier S Natalia S Adriani martyris coniuge expressa, school play (Vienna, 1677)
Keyboard:
- 11 toccatas (8 a separate cycle, 3 more in another source)
- 6 canzonas
- 5 versets
- 4 suites
- 2 preludes
Other instrumental:
- Canzona for two violins, viola da gamba and basso continuo
- 2 sonatas for two violins, viola da gamba and basso continuo
- Sonata modi dorii for two violins, viola da gamba and basso continuo
- Sonata for two violins, two violas and basso continuo
