While serving an assistant at Halle, he made improvements on Hermann Welcker’s procedure for measurement of blood volume.
Three of his famous students at Breslau were Karl Weigert (1845-1904), Ivan Petrovich Pavlov (1849-1936), and Albert Wojciech Adamkiewicz (1850-1921).
His laboratory was the source of voluminous contributions by himself, his pupils, or his assistants to Pflügers Archiv on a large variety of special topics in the field of his studies.
He studied the stomach's gastric glands and the processes it used to produce pepsin and hydrochloric acid.
Heidenhain conducted scientific studies of hypnotism, having been impressed by the public hypnotist, Carl Hansen.