The morphology of the intrinsic innervation of internal anal sphincter (IAS) in Hirschsprung's disease (HSCR) and allied disorders has not been clearly defined. At the time of IAS myectomy, specimens of the IAS were taken from four patients with HSCR, five patients with intestinal neuronal dysplasia (IND), five patients with IAS achalasia, and two patients with hypoganglionosis. Specimens also were taken from five normal controls. The specimens were examined using neural cell adhesion molecule (NCAM) immunohistochemistry, NADPH-diaphorase histochemistry, and acetylcholinesterase (AChE) histochemistry. The number of AChE-positive nerve fibers was markedly increased in the IAS of patients with HSCR, IND, and IAS achalasia compared with controls. NCAM and NADPH-diaphorase activity was absent or markedly reduced in the IAS of patients with HSCR, IND, and IAS achalasia. The IAS of patients with hypoganglionosis show markedly reduced NCAM and NADPH-diaphorase activity and occasional AChE-positive nerve fibers. These findings show that patients with HSCR, IND, hypoganglionosis, or IAS achalasia have abnormal innervation of the IAS and this may contribute to disturbances in gut motility in these conditions.