Interstitial cells of Cajal (ICCs) in the gastrointestinal tract are a group of cells interacting with enteric neurons and smooth muscle cells. They serve as mediators of neurotransmission and pacemakers of the peristaltic movement of the gut. Previous investigations on patients with Hirschsprung’s disease and mice with aganglionic megacolon showed contrasting results on the relationship between the abnormalities of ICCs and enteric neurons. In order to ascertain whether the development of ICCs is also perturbed in the aganglionic segment of the gut, we used Dominant megacolon (Dom) mice as an animal model and an antibody specific to c-kit (a tyrosine kinase receptor expressed in ICCs) to examine the spatial distribution of ICCs in the developing and adult colon. Our results showed that in the wild-type adult colon, ICCs were bipolar in shape in the smooth muscle layer and dense networks of ICCs were observed in the myenteric and deep muscular plexuses, whereas in the aganglionic colon of Dom heterozygous mice, no ICCs could be found in the smooth muscle layer and disrupted patterns of ICC networks were observed in the myenteric and deep muscular plexuses. On 14.5 days of development, the levels of expression of c-kit and its ligand (stem cell factor) were similar in the wild-type, heterozygous and homozygous Dom embryos. However, by 18.5 days, the numbers of ICCs were greatly reduced in the myenteric and submucosal plexuses of the terminal colon of the heterozygous embryos comparing with the wild-type counterparts. Based on our results, we postulate that the abnormal development of ICCs may disrupt the neurotransmission and pacemaker activity of the gut, leading to interrupted peristalsis.