Comment. in lib. III decretalium (Ingolstadt, 1629)
De Sponsalibus et Matrimonio (Ingolstadt, 1613)
A complete edition of his canonical writings appeared in Leuven in 1649 and in Cologne in 1662.
His major historical work was Antiquae Lectiones, seu antiqua monumenta ad historiam mediae aetatis illustrandam (6 volumes, Ingolstadt, 1601–1604). In 1608 a seventh volume, Promptuarium Ecclesiasticum, was added by way of supplement. The Catholic Encyclopedia describes the work as disorganized and containing "much matter of minor value"; Basnage produced a heavily edited version under the title Thesaurus Monumentorum ecclesiasticorum et historicorum (7 vols., Antwerp, 1725).
Canisius edited for the first time the Chronica Victoris Episcop. Tunnunensis et Joannis Episcop. Biclariensis, and the Legatio Luitprandi (Ingolstadt, 1600). He also produced an edition of the Historiae miscellae Pauli Diaconi (Ingolstadt, 1603).