• Mysterium Cosmographicum
  The Sacred Mystery of the Cosmos
  
  • 1596
  • 1621 - 2nd edition
• De Fundamentis Astrologiae Certioribus
  On Firmer Fundaments of Astrology
  1601
• Astronomiae Pars Optica
  The Optical Part of Astronomy
  1604
• De Stella nova in pede Serpentarii
  On the New Star in Ophiuchus's Foot
  1606
• Astronomia nova
  New Astronomy
  1609 Tertius Interveniens
  Third-party Interventions
  1610
• Dissertatio cum Nuncio Sidereo
  Conversation with the Starry Messenger
  1610
• Dioptrice (1611)
• De nive sexangula
  On the Six-Cornered Snowflake
  1611
• De vero Anno, quo aeternus Dei Filius humanam naturam in Utero benedictae Virginis Mariae assumpsit (1614)
• Eclogae Chronicae (1615, published with Dissertatio cum Nuncio Sidereo)
• Nova stereometria doliorum vinariorum New Stereometry of Wine Barrels
  1615
• Ephemerides nouae motuum coelestium (1617-30)
• Epitome astronomiae Copernicanae
  Epitome of Copernican Astronomy)
  published in three parts from 1618 to 1621 contains the first version in print of Kepler's third law of planetary motion
  intended as a textbook
  Divided into seven books
  In Book IV he supported the Copernican cosmology
  Book V - mathematics
  published in parallel with Harmonices Mundi (1619)
  Books V to VII appearing in 1621
  first use of the term 'inertia'
  Book I was put on the Index of Prohibited Books on 28th of February 1619
• Harmonices Mundi
  Harmony of the Worlds) (1619)
• Tabulae Rudolphinae
  Rudolphine Tables) (1627)
• Somnium
  The Dream
  (1634)

A critical edition of Kepler's collected works (Johannes Kepler Gesammelte Werke, KGW) in 22 volumes is being edited by the Kepler-Kommission (founded 1935) on behalf of the Bayerische Akademie der Wissenschaften.

• Vol. 1: Mysterium Cosmographicum. De Stella Nova. Ed. M. Caspar. 1938, 2nd ed. 1993. Paperback ISBN 3-406-01639-1.
• Vol. 2: Astronomiae pars optica. Ed. F. Hammer. 1939, Paperback ISBN 3-406-01641-3.
• Vol. 3: Astronomia Nova. Ed. M. Caspar. 1937. IV, 487 p. 2. ed. 1990. Paperback ISBN 3-406-01643-X. Semi-parchment ISBN 3-406-01642-1.
• Vol. 4: Kleinere Schriften 1602–1611. Dioptrice. Ed. M. Caspar, F. Hammer. 1941. ISBN 3-406-01644-8.
• Vol. 5: Chronologische Schriften. Ed. F. Hammer. 1953. Out-of-print.
• Vol. 6: Harmonice Mundi. Ed. M. Caspar. 1940, 2nd ed. 1981, ISBN 3-406-01648-0.
• Vol. 7: Epitome Astronomiae Copernicanae. Ed. M. Caspar. 1953, 2nd ed. 1991. ISBN 3-406-01650-2, Paperback ISBN 3-406-01651-0.
• Vol. 8: Mysterium Cosmographicum. Editio altera cum notis. De Cometis. Hyperaspistes. Commentary F. Hammer. 1955. Paperback ISBN 3-406-01653-7.
• Vol 9: Mathematische Schriften. Ed. F. Hammer. 1955, 2nd ed. 1999. Out-of-print.
• Vol. 10: Tabulae Rudolphinae. Ed. F. Hammer. 1969. ISBN 3-406-01656-1.
• Vol. 11,1: Ephemerides novae motuum coelestium. Commentary V. Bialas. 1983. ISBN 3-406-01658-8, Paperback ISBN 3-406-01659-6.
• Vol. 11,2: Calendaria et Prognostica. Astronomica minora. Somnium. Commentary V. Bialas, H. Grössing. 1993. ISBN 3-406-37510-3, Paperback ISBN 3-406-37511-1.
• Vol. 12: Theologica. Hexenprozeß. Tacitus-Übersetzung. Gedichte. Commentary J. Hübner, H. Grössing, F. Boockmann, F. Seck. Directed by V. Bialas. 1990. ISBN 3-406-01660-X, Paperback ISBN 3-406-01661-8.
• Vols. 13–18: Letters:
• Vol. 13: Briefe 1590–1599. Ed. M. Caspar. 1945. 432 p. ISBN 3-406-01663-4.
• Vol. 14: Briefe 1599–1603. Ed. M. Caspar. 1949. Out-of-print. 2nd ed. in preparation.
• Vol 15: Briefe 1604–1607. Ed. M. Caspar. 1951. 2nd ed. 1995. ISBN 3-406-01667-7.
• Vol. 16: Briefe 1607–1611. Ed. M. Caspar. 1954. ISBN 3-406-01668-5.
• Vol. 17: Briefe 1612–1620. Ed. M. Caspar. 1955. ISBN 3-406-01671-5.
• Vol. 18: Briefe 1620–1630. Ed. M. Caspar. 1959. ISBN 3-406-01672-3.
• Vol. 19: Dokumente zu Leben und Werk. Commentary M. List. 1975. ISBN 978-3-406-01674-5.
• Vols. 20–21: manuscripts
• Vol. 20,1: Manuscripta astronomica (I). Apologia, De motu Terrae, Hipparchus etc. Commentary V. Bialas. 1988. ISBN 3-406-31501-1. Paperback ISBN 3-406-31502-X.
• Vol. 20,2: Manuscripta astronomica (II). Commentaria in Theoriam Martis. Commentary V. Bialas. 1998. Paperback ISBN 3-406-40593-2.
• Vol. 21,1: Manuscripta astronomica (III) et mathematica. De Calendario Gregoriano. In preparation.
• Vol. 21,2: Manuscripta varia. In preparation.
• Vol. 22: General index, in preparation.

The Kepler-Kommission also publishes Bibliographia Kepleriana (2nd ed. List, 1968), a complete bibliography of editions of Kepler's works, with a supplementary volume to the second edition (ed. Hamel 1998).