BACKGROUND: Esophageal achalasia (EA) is a rare disease in children, the etiology and pathogenesis of which remain controversial. Previous studies have suggested that a specific class of interstitial cells of Cajal (ICC) act as mediators in nitrergic inhibitory neurotransmission in the lower esophageal sphincter (LES). The aim of this investigation is to clarify the status of ICC and nitrergic inhibitory neurons in the LES of EA using immunohistochemistry. METHODS: Specimens were obtained from two patients with EA (aged 6 and 10 years) and two patients with esophageal carcinoma (aged 56 and 63 years) not involving the lower esophagus as controls. Immunohistochemistry was used to study the distribution of ICC and nitrergic inhibitory neuron. RESULTS: The LES contains the c-kit positive ICC in the muscle layers, which form close relationships with nitric oxide synthase (NOS)-containing nerve fibers in the controls. The distribution of ICC was almost the same between samples with EA and controls. However, such nerve fibers were absent in EA with a longer duration of the symptoms, but were reduced in a shorter duration. CONCLUSIONS: Decreased nitrergic inhibitory neurotransmission to ICC in LES is a possible cause of sphincter achalasia in pediatric patients with EA. The decrease in NOS-positive neurons of patients with achalasia may be gradual, which may account for the long duration of symptoms prior to treatments. Further advancement of esophageal motility damage was suspected in pediatric EA.