Numerous advances in understanding the molecular basis of congenital heart disease have been published in the past year. Highlights are reviewed, focusing on two major topics: genetic syndromes and cardiac organogenesis. Genetic syndromes are discussed in the context of complementary data from targeted mutations in animals and genetic mapping studies in humans. These include the DiGeorge, Holt-Oram, Alagille, familial primary pulmonary hypertension, and Noonan syndromes. Novel concepts in cardiac organogenesis are discussed, including the existence and contribution of an anterior heart field to the developing cardiac outflow tract, novel cell-cell signaling involving migrating neural crest, the origins of the conduction system and initial embryonic heartbeat, and the possibility of a population of cardiac stem cells in the adult heart. The studies reviewed have potential clinical relevance in the near future and will be of interest to the clinician interested in congenital heart disease.