Gegenbaur's book Grundzüge der vergleichenden Anatomie (1859; Elements of Comparative Anatomy) became the standard textbook, at the time, of evolutionary morphology, emphasizing that structural similarities among various animals provide clues to their evolutionary history. Carl Gegenbaur noted that the most reliable clue to evolutionary history is homology, the comparison of anatomical parts which have a common evolutionary origin.
The work by which Gegenbaur is best known is his Grundriss der vergleichenden Anatomie (Leipzig, 1874; 2nd edition, 1878), translated into English by W. F. Jeffrey Bell (as 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, with the foreleg of a horse, and with 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 skull-vertebrae theory: 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.
In 1858, the physician Ernst Haeckel studied under Carl Gegenbaur at Jena, receiving a doctorate in zoology (after his medical degree), and became a professor at the same institution, the University of Jena (see: Ernst Haeckel). Ernst Haeckel expanded on the ideas of Gegenbaur while advocating the concepts of Charles Darwin.
In 1861 he published Ueber den Bau und die Entwickelung der Wirbelthier-Eier mit partielleer Dotterbildung."Proof that the ovum is unicellular in all vertebrates" (Arch. Anat. Phys., 1861.8: 461-529 ) a fundamental proof in embryology.
Gegenbaur learned techniques as a student of Albert von Kölliker, Rudolf Virchow, Heinrich Müller and Franz Leydig (1821-1905). . Carl Gegenbaur had a strong influence on his environment, with his colleagues Matthias Jakob Schleiden, Emil Huschke, Ernst Haeckel, and Hermann Klaatsch (1863-1916). Carl Gegenbaur also influenced his students, including: Max Fürbringer, Richard Hertwig, Oskar Hertwig, Emil Rosenberg, Ambrosius Hubrecht, Johan Erik Vesti Boas (1855-1935), Hans Friedrich Gadow, M. Sagemehl, N. Goronowitsch, H. K. Corning, C. Röse and S. Paulli.
Gegenbaur's research program of comparative morphology incorporating ontogeny and phylogeny is still evident in the burgeoning field of evolutionary developmental biology (evo-devo).