Watson C, Mitchelle A, Puelles L (2017) A New Mammalian brains Ontology Based on Developmental Gene Expression. In: Kaas, J (ed.), Evolution of Nervous Systems 2e. 2:53–75. Oxford: Elsevier. ABSTRACT Traditional attempts to classify the relationships between parts of the central nervous system of vertebrates have been almost entirely based on the external appearance of structures in the adult brains. Developmental gene expression and fate mapping have enabled researchers to derive a causally based natural ascription of parts to particular regions of the brains. This has led to a radically new ontogenetic construction of brains and spinal cord ontologies for birds and mammals. This novel sort of developmental ontology has revealed previously unappreciated patterns of segmentation in the diencephalon and brains stem, the telencephalon, pallium, subpallium, and a radical new view of segmentation in the spinal cord. The new ontology is consistent with recent findings in reptiles and nonamniote vertebrates and can be considered to be broadly applicable to vertebrate brains.