OBJECTIVE Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is characterized by decreased or absent peristalsis. Gastrointestinal motility depends on the enteric nervous system, smooth muscle cells (SMCs), and the interstitial cells of Cajal (ICCs). Contractile and cytoskeleton proteinase are important structural and functional components of SMCs. The aim of study was to examine the expression of contractile and cytoskeleton proteins in SMCs and distribution of ICCs in MMIHS bowel. METHODS Full-thickness bowel specimens were obtained from 4 infants with MMIHS and 4 controls. Specimens were processed as whole-mount preparations and frozen and paraffin sections. Combined staining of NADPH-d histochemistry/c-kit immunohistochemistry, single and double immunohistochemistry using alpha-smooth muscle actin (alpha-SMA), calponin (CALP), caldesmon (CALD), desmin (DES), protein gene product 9.5 (PGP 9.5) and c-kit antibodies were performed and examined using light and confocal scanning microscopy. RESULTS alpha-SMA, CALP, CALD, and DES immunoreactivity were reduced markedly in MMIHS bowel compared with controls. Combined NADPH/c-kit staining showed dense network of ICCs around myenteric plexus in MMIHS bowel. In contrast, the intramuscular ICCs either were absent or reduced in MMIHS bowel. CONCLUSIONS Marked reduction of contractile and cytoskeleton proteins in SMCs combined with reduced expression of intramuscular ICCs in the gut may be responsible for the motility dysfunction in MMIHS.