For more than a century, scientists had attempted to determine the exact nature and location of the mammalian egg. During his research in 1826, Baer discovered the mammalian egg by identifying a yellowish spot within the ovarian follicle visible only with a microscope. He developed this idea in his 1827 treatise, De ovi mammalium et hominis genesi (On the Origin of the Mammalian and Human Ovum).
Baer studied the embryonic development of animals, discovering the blastula stage of development and the notochord. Together with Heinz Christian Pander and based on the work by Caspar Friedrich Wolff, Baer described the germ layer theory of development (ectoderm, mesoderm, and endoderm) as a principle in a variety of animal species. He summarized his findings in his two-volume textbook entitled Über Entwickelungsgeschichte der Thiere (On the Development of Animals) which he published between 1828 and 1837, laying the foundation for comparative embryology.