The period of transition from the aquatic to the terrestrial environment involved the development of a greater degree of activity, and the regions of the reptile brain most affected by these changes were the telencephalon, thalamus, mesencephalic roof and cerebellum. The aim was to identify and morphologically map, internally and externally, the regions of the encephalon in different reptile species and Podocnemis expansa embryos. Juvenile reptile species (P. expansa, Podocnemis unifilis, Phrynops geoffroanus, Melanosuchus niger, Bothrops jararaca and Salvator merianae) and P. expansa eggs incubated artificially until stage 25 were used, after which the brain was euthanised and removed. For macroscopic analysis, the brains were fixed in formaldehyde, and for microscopic analysis of the embryos, semi-serial cryosections were made and stained with eosin and counterstained with Nissl. It was concluded that in B. jararaca there is the presence of a fourth ventricle and a choroid plexus internal to the encephalon, a rudimentary cerebellum and the absence of the accessory nerve (XI), and the embryos have a prominent dorsal ventricular crest and tegmentum nuclei in the ventral region of the bulb.