The role of traditions, revision of dogmatic concepts, and emergence of novel theories in the investigations of the vertebrate brain evolution on the bases of modern neuroscientific data represent the objective of the present paper. Problems of homology, encephalization, recapitulation, dissolution, and the significance of their revision for understanding the brain evolution are considered. Arguments for equal importance in studying consequences of both phylogenetic and divergent adaptive evolution are presented. Comparative study of functional mechanisms is suggested as a perspective trend of the evolutionary physiology. It will be a valuable tool both for understanding the brain evolution and for applied investigations in neurobiology and medicine.