In the past, attempts to create a hierarchical classification of brain structures (an ontology) have been limited by the lack of adequate data on developmental processes. Recent studies on gene expression during brain development have demonstrated the true morphologic interrelations of different parts of the brain. A developmental ontology takes into account the progressive rostrocaudal and dorsoventral differentiation of the neural tube, and the radial migration of derivatives from progenitor areas, using fate mapping and other experimental techniques. In this review, we used the prosomeric model of brain development to build a hierarchical classification of brain structures based chiefly on gene expression. Because genomic control of neural morphogenesis is remarkably conservative, this ontology should prove essentially valid for all vertebrates, aiding terminological unification. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.