Here are some of his major works:
* "Die mehrstimmige Musik des Mittelalters und der Renaissance" (Polyphonic Music of the Middle Ages and Renaissance): This is his most important work and a cornerstone of polyphony research. It explores the evolution of polyphony from the Middle Ages to the Renaissance, providing a comprehensive analysis of styles, techniques, and composers.
* "Palestrina": A detailed study of the life and works of Giovanni Pierluigi da Palestrina, one of the most important Renaissance composers.
* "The Style of Palestrina and the Dissonance": This work examines the specific techniques and rules that Palestrina used in his compositions.
* "The Counterpoint: The Polyphonic Vocal Style of the 16th Century": A book that provides a practical guide to counterpoint, based on the principles of Renaissance polyphony.
* "The History of Vocal Polyphony": A comprehensive account of the development of vocal polyphony from the early Middle Ages to the 18th century.
Jeppesen also wrote numerous articles, essays, and lectures on music history, counterpoint, and the works of specific composers. He was a prolific writer and a respected authority on Renaissance polyphony.