In 1886 Bardeleben was founder of the Anatomischer Anzeiger (Annals of Anatomy), a journal that is considered to be one of the better publications on anatomical morphology. The journal contains many original treatises on topographic and clinical anatomy, embryology, cell and tissue research, as well as microscopic and "submicroscopic" biology.
In 1892 he published the collected anatomical writings of Johann Wolfgang von Goethe, titled "Goethe als Anatom". Other significant writings by Bardeleben are:
Atlas der topographischen Anatomie des Menschen: für Studierende und Ärzte (Atlas of applied (topographical) human anatomy for students and practitioners); with Heinrich Haeckel, in collaboration with Fritz Frohse (1871–1916) and Theodor Ziehen (1862–1950).
Anleitung zum Praeparieren auf dem Sociersaale (1884).