The enteric nervous system (ENS) is composed of neurons and glial cells, organized as interconnected ganglia within the gut wall, which controls persistalsis of the gut wall and secretions from its glands. The Ret receptor tyrosine kinase is expressed throughout enteric neurogenesis and is required for normal ENS development; humans with mutations in the RET locus have Hirschsprung disease (HSCR, an absence of ganglia in the colon), and mice lacking Ret have total intestinal aganglionosis. The Ret mutant mouse provides a tool for identifying genes implicated in development of the ENS. By using RNA from WT and Ret mutant (aganglionic) gut tissue and DNA microarrays, we have conducted a differential screen for ENS-expressed genes and have identified hundreds of candidate ENS-expressed genes. Forty-seven genes were selected for further analysis, representing diverse functional classes. We show that all of the analyzed genes are expressed in the ENS and that the screen was sensitive enough to identify genes marking only subpopulations of ENS cells. Our screen, therefore, was reliable and sensitive and has identified many previously undescribed genes for studying ENS development. Moreover, two of the genes identified in our screen Arhgef3 and Ctnnal1, have human homologues that map to previously identified HSCR susceptibility loci, thus representing excellent candidates for HSCR genes. This comprehensive profile of ENS gene expression refines our understanding of ENS development and serves as a resource for future developmental, biochemical, and human genetic studies.T he enteric nervous system (ENS) is composed of a vast number of neurons and glial cells, which form interconnected ganglia that control the contractility of the smooth muscle of the gut wall and the secretory activity of its glands (1). The ENS is derived from vagal and sacral enteric neural crest cells (ENCs), which invade the foregut and hindgut, respectively (2, 3). Once situated within the gut, ENCs migrate along the developing bowel, proliferate, and differentiate to form many different neuronal subtypes and make synaptic connections (4, 5). Migration of ENCs within the gut requires signaling between these cells and the gut environment and depends on dynamic changes in cell shape and adhesive properties. How cell shape and adhesion are controlled to allow regulated and directed migration of ENCs currently is unknown. Furthermore, how cell fate decisions are controlled to specify the correct number and subtypes of neurons and glial cells within ENS ganglia or how correct synaptic circuits are established also is unknown.Genetic studies in mouse and human have identified several genes whose function is required for normal ENS development (6, 7). For example, the Ret receptor tyrosine kinase is expressed in ENCs during migration into the gut and persists during later ENS development (8). Humans carrying mutations in RET develop congenital megacolon [Hirschsprung disease (HSCR) OMIM 142623; ref. 7], which is characterized by the absence of enteric ga...