This is a list of the musical compositions of Michael Haydn sorted by genre, and then chronologically when year of composition is indicated, otherwise alphabetically. The numbering in parentheses starting with the capital letter P refers to Perger catalogue. The MH numbers refer to the Sherman & Thomas catalog of 1993.

Instrumental music

Symphonies

All of Michael Haydn's symphonies have at least 2 oboes, 2 bassoons, 2 horns and strings (first and second violins, violas and basses, but no cellos). Some symphonies add more instruments, such as trumpets and timpani in some of the C major symphonies. They are usually either in three or four movements. Continuo is explicitly called for only in the earlier works, and the modern editions usually follow the old practice of putting the bassoons, basses and the left hand of the continuo on a single staff below the violas' staff. Many of Michael Haydn's symphonies were at first attributed to Joseph Haydn. Only one of them was first attributed to Wolfgang Amadeus Mozart as his Symphony No. 37 (K. 444).

Concertos

With two exceptions, it is believed all of Haydn's concerti were written in Salzburg.

Serenades

Incidental music

Ballets

Dances

Marches

Quintets

Quartets

The authenticity of the six string quartets MH 308–313 is under dispute.

Trio sonatas

Duo sonatas

Hieronymus Graf von Colloredo commissioned Haydn to write six duos for violin and viola. Haydn fell ill after completing the fourth, so he asked Mozart to write the other two (K. 423 and K. 424). The set of six was presented as all Haydn's, and Colloredo was unable to "detect in them Mozart's obvious workmanship."

Solo sonatas

Keyboard

Unknown instrumentation

Sacred vocal music

Antiphons

Sacred Cantatas

Canticles

Graduals

Hymns

Masses

Motets

Offertories

Oratorios

Psalm settings

Requiem

Other

Secular vocal music

Arias

Canons

Cantatas

Part-songs

Operas

Serenatas

Singspiele

Songs