cells of Cajal (ICC) have important functions in regulation of motor activity in the gastrointestinal tract. In murine small intestine, ICC are gathered in the regions of the myenteric plexus (ICC-MY) and the deep muscular plexus (ICC-DMP). These two classes of ICC have different physiological functions. ICC-MY are pacemaker cells and generate the slow-wave electrical rhythmicity of gastrointestinal organs. ICC-DMP form synaptic connections with the varicose nerve terminals of enteric motor neurons and are involved in reception and transduction of motor neurotransmission. Gene expression underlying specific functions of ICC classes is incompletely understood. In the present study, we used recently developed highly selective techniques to isolate the two functional ICC classes from enzymatically dispersed intestinal muscles by fluorescence-activated cell sorting. The transcriptomes of ICC-MY and ICC-DMP were investigated using oligonucleotide microarray analysis. Differential expression of functional groups of genes defined by standard gene ontology terms was also studied. There were substantial numbers of genes expressed more abundantly in ICC than in the tunica muscularis, and we also detected marked phenotypic differences between ICC-MY and ICC-DMP. Notably, genes related to cell junction, process guidance, and vesicle trafficking were upregulated in ICC. Consistent with their specific functions, metabolic and Ca 2ϩ transport genes were relatively upregulated in ICC-MY, whereas genes for signaling proteins involved in transduction of neurotransmitter functions were relatively upregulated in ICC-DMP. Our results may lead to the identification of novel biomarkers for ICC and provide directions for further studies designed to understand ICC function in health and disease.Affymetrix Mouse Genome 430.2 GeneChips; Bioconductor; enteric nervous system; ion channel; signal transduction MOTOR PATTERNS of the gastrointestinal (GI) tract require the coordinated contractions of the smooth muscle cell component of the organs. One level of coordination comes from the fact that the smooth muscle cells are electrically coupled, and their electrical activity is driven by pacemaker cells known as interstitial cells of Cajal (ICC) that lie in the plane of the myenteric plexus between the circular and longitudinal muscle layers (ICC-MY) (16, 58). ICC-MY are electrically coupled to each other via gap junctions and form a network of cells that extends around the circumference and along the length of the small intestine (1, 39, 58). The ICC-MY network is electrically coupled to smooth muscle cells of both layers, providing a low-resistance pathway for the conduction of pacemaker activity to the musculature (9). ICC-MY possess the ionic conductances necessary to initiate electrical slow waves and to propagate these events actively (cf. Ref. 43).A second level of control of GI motor function comes from the intrinsic motor neurons arising from enteric ganglia. Both inhibitory and excitatory motor neurons innervate the muscle layers, an...