Carl Gegenbaur (August 21, 1826 - June 14, 1903) was a German anatomist.

Gegenbaur was born at Wurzburg, the university of which he entered as a student in 1845. After taking his degree in 1851 he spent some time in travelling in Italy and Sicily, before returning to Wurzburg as Privatdocent in 1854. In 1855 he was appointed extraordinary professor of anatomy at Jena, where after 1865 his fellow-worker, Ernst Haeckel, was professor of zoology, and in 1858 he became the ordinary professor. In 1873 he was appointed to Heidelberg, where he was professor of anatomy and director of the Anatomical Institute until his retirement in 1901. He died at Heidelberg.

The work by which perhaps he is best known is his Grundriss der vergieichenden Anatomk (Leipzig, 1874; 2nd edition, 1878). This was translated into English by W. F. Jeffrey Bell (Elements of Comparative Anatomy, 1878), with additions by E. Ray Lankester. While recognizing the importance of comparative embryology in the study of descent, Gegenbaur laid stress on the higher value of comparative anatomy as the basis of the study of homologies, i.e. of the relations between corresponding parts in different animals, as, for example, the arm of man, the foreleg, of the horse and the wing of a fowl. A distinctive piece of work was effected by him in 1871 in supplementing the evidence adduced by Huxley in refutation of the theory of the origin of the skull from expanded vertebrae, which, formulated independently by Goethe and Oken, had been championed by Owen. Huxley demonstrated that the skull is built up of cartilaginous pieces; Gegenbaur showed that in the lowest (gristly) fishes, where hints of the original vertebrae might be most expected, the skull is an unsegmented gristly brain-box, and that in higher forms the vertebral nature of the skull cannot be maintained, since many of the bones, notably those along the top of the skull, arise in the skin.

Other publications by Gegenbaur include a Text-book of Human Anatomy (Leipzig, 1883, new ed. 1903), the Epiglottis (1892) and Comparative Anatomy of the Vertebrates in relation to the Invertebrates (Leipzig, 2 vols., 1898-1901). In 1875 he founded the Morphologisches Jahrbuch, which he edited for many years. In 1901 he published a short autobiography under the title Erlebtes und Erstrebtes.