Rapid advances in cardiovascular science have expanded our knowledge of the mechanisms of heart development. Epidemiologists have defined the prevalence of congenital cardiovascular malformations, developmental biologists have delineated cascades of cell lineage, and molecular geneticists have identified mutations and loci associated with familial heart and vascular defects. We are well on the way to a molecular understanding of congenital cardiovascular malformations. Thus, it seems appropriate to review the pathogenetic classification of congenital cardiovascular malformations in light of this new clinical and scientific evidence. This schema serves as a template for the scientist to organize clinical information relevant to the pathogenesis of cardiac defects and as a tool for the clinician in approaching the difficult task of counseling parents of children with congenital cardiovascular malformations.