Esophageal atresia is a common and serious developmental anomaly, of which the causes remain largely unknown. Studies in vertebrate models indicate the importance of the sonic hedgehog pathway in esophageal atresia, but its relevance to the human condition remains to be defined. Now, three genes have been identified that cause syndromic forms of esophageal atresia when mutated. NMYC and SOX2 are transcription factors, whereas CHD7 is encoded by a chromodomain helicase DNA-binding gene, important for chromatin structure and gene expression. These new genes broaden our view of human foregut development.