After leaving Tartu, he continued his education in Berlin, Vienna, and Würzburg, where Ignaz Döllinger introduced him to the new field of embryology.

While embryology had kept his attention in Königsberg, then in Russia von Baer engaged in a great deal of field research, including the exploration of the island Novaya Zemlya.

Together with Heinz Christian Pander and based on the work by Caspar Friedrich Wolff, he described the germ layer theory of development (ectoderm, mesoderm, and endoderm) as a principle in a variety of species, laying the foundation for comparative embryology in the book Über Entwickelungsgeschichte der Thiere (1828).

Baer recorded the importance of permafrost research even before 1837 when observing in detail the geothermal gradient from a 116.7 m deep shaft in Yakutsk.

At the end of the 1830s, he recommended sending expeditions to explore permafrost in Siberia and suggested Alexander von Middendorff as leader.

The German title is „Materialien zur Kenntniss des unvergänglichen Boden-Eises in Sibirien“ (=materials for the knowledge of the perennial ground ice in Siberia).

Well known was his paper "On the Ground Ice or Frozen Soil of Siberia", published in the Journal of the Royal Geographical Society of London (1838, pp.

Russian authors usually relate with it the name Alexander von Middendorff (1815–1894), as he did much scientific work during the years 1842–1845 concerning permafrost on Taimyr Peninsula and in East-Siberia.

They even believed, that the scepticism about the permafrost findings and publications of Middendorff would not have risen, if Baer's original "materials for the study of the perennial ground-ice" would have been published in 1842 as intended.

The first post-World War major contact between groups of senior Russian and American frozen ground researchers took place in November 1963 in Yakutsk.However, Baer's permafrost textbook remained still undiscovered.

Baer's text is introduced with detailed comments and references on additional 66 pages written by the Estonian historian Erki Tammiksaar.

The work is fascinating to read, because both Baer's observations on permafrost distribution and his periglacial morphological descriptions are largely still correct today.

From his studies of comparative embryology, Baer had believed in the transmutation of species but rejected later in his career the theory of natural selection proposed by Charles Darwin.

He produced an early tree-like branching diagram illustrating the sequential origins of derived character states in vertebrate embryos during ontogeny that implies a pattern of phylogenetic relationship.

[28] A statue honouring him can be found on Toome Hill in Tartu, as well as at Lasila manor, Estonia, and at the Zoological Museum in St Petersburg, Russia.