Recent work is providing new insights into molecular mechanisms of digestive system development and their alteration in clinically significant disorders. An understanding of these mechanisms has largely been gained through the use of animal models, because many of the basic processes required in embryogenesis are functionally conserved among species. Such conserved factors include cell-cell signaling pathways and the regulation of gene expression. Disruption of these pathways have been implicated in several congenital disorders of the digestive system, including Hirschsprung disease, malrotation, altered sphincter development, Meckel diverticulum, biliary atresia, Alagille syndrome, pancreatic heterotopias, and pancreatic agenesis. In this review, we highlight recent studies in digestive system development, which elucidate mechanisms underlying congenital disorders of the human digestive system.