This review tries to establish a synthesis between the comparative/morphological approach and the molecular analysis of ontogenetic processes in development and evolution. We use the formation of the nervous system in metazoans as a paradigm to point out that highly conserved molecular mechanisms may be responsible to generate tissues and organ systems in bilateria. We discuss the conserved role of the Hox genes in anterior- posterior patterning, the function of the Achaete-scute genes and of the Notch/Delta signalling cascade in determining neural fates and the role of the BMP-4/Dpp-signalling pathway in positioning the neuroectoderm along the dorso-ventral axis of vertebrates and insects. We try to demonstrate that the evolution of complex body structures is based on modifying ontogenetic processes.