Waldeyer-Hartz was born in Hehlen, Germany, on October 6, 1836. He began his college education in the natural sciences at Göttingen in 1856, but later moved to Greifswald and eventually to Berlin to complete his studies. Under the influence of the great anatomist Friedrich Henle (1809-1885) at Göttingen, Waldeyer-Hartz turned his attention to anatomy and medicine. He received his medical degree from Berlin in 1862 and later held a number of prestigous posts at such universities as Strasbourg and Berlin.

Waldeyer-Hartz's accomplishments covered a wide range of topics. His name is preserved in anatomy for his studies of the ring of lymphoid tissue that surrounds the pharynx, Waldeyer's ring. He also introduced the term chromosome for the cellular structures earlier described by Walther Flemming. Other research included studies of the ovary and ovum, the germinal epithelium, and the spinal cord of the gorilla. Some of his earliest studies on cancer earned him widespread fame, and he was called upon to consult on cancer for important personages, including the Emperor Frederick III.

The contribution for which Waldeyer-Hartz is perhaps best known is his theory of nerve transmission. In the early 1890s, he developed a theory that the nervous system consists of discrete cells, for which he coined the term neuron. He argued that the projections of individual neurons lay very close to each other, but do not actually come into contact. Although he did no original research in this field himself, his theory provided a valuable model for the investigations of such scientists as Camillo Golgi and Charles Scott Sherrington, who later studied the nervous system and the gap between neurons, eventually named the synapse.