Interstitial cells of Cajal (ICCs) are pacemaker cells which are densely distributed throughout the whole gastrointestinal tract. ICCs have important functions in neurotransmission, generation of slow waves and regulation of mechanical activities in the gastrointestinal tract, especially for the coordinated gastrointestinal peristalsis. Therefore, a loss of ICCs could result in gastrointestinal motor dysfunction. In recent years c-kit labeling has been widely used to study pathological changes of ICCs in gastrointestinal motility disorders. Paediatric gastrointestinal motility disorders such as hypertrophic pyloric stenosis, Hirschsprung's disease, total colonic aganglionosis, hypoganglionosis, intestinal neuronal dysplasia, internal anal sphincter achalasia, megacystis microcolon intestinal hypoperistalsis syndrome have been reported to be associated with loss or deficiency of ICCs networks. This review describes the distribution of ICCs in the normal gastrointestinal tract and its altered distribution in intestinal motility disorders of childhood.