In the early 19th century Karl Ernst von Baer initiated a new research program searching for the mechanisms by which an egg transforms itself into an embryo. August Rauber (1841 1917) took up this challenge. He considered the phylogenetic principle as the right tool to explain the similitude of embryogenetic processes. In extending Baer's approach, he combined comparative embryology and histology in his studies of avian and mammalian embryos. His earlier work demonstrated that the two-layered chick embryo is a modified gastrula and not a "disc" as Wilhelm His had claimed. From the 1880s onwards, he concentrated on the issue of how the development of germ layers is related to tissue differentiation. To address this, he studied the blastopore, epiblast, primitive streak, teratology and the relative importance of nucleus and cytoplasm in heredity. This paper reconstructs some of Rauber's work and concludes that his observations and reflections constituted a new approach combining embryology and histology with "phylogenetic" reasoning.