BACKGROUND/AIMS: To obtain accurate diagnosis for Hirschsprung's disease (HD) and its allied disorders such as hypoganglionosis (Hypo) and intestinal neuronal dysplasia (IND) in childhood patients with chronic constipation, we studied the histology of childhood patients with refractory constipation accompanied by abdominal distension and pain. METHODOLOGY: Based on clinical signs and symptoms noted on admission, all of 109 patients (60 males and 49 females, aged 2-15 years with a mean age of 9.8 years) were suspected to have chronic refractory constipation. To obtain accurate histological diagnosis in childhood patients with chronic refractory constipation, we performed rectal biopsies on these patients. Tissue samples were frozen and 12-microm sections were stained with acetylcholinesterase (AChE) by the method of Karnovsky and Roots, and with nicotinamide adenine dinucleotide phosphate (NADPH)-diaphorase by the modified Scherer-Singler's method. RESULTS: On the basis of histological studies using rectal biopsies, 20 cases were diagnosed with Hypo, 5 with HD, 2 with intestinal neuronal dysplasia (IND), and 82 with normal findings. The incidence of normal cases was significantly greater than that of allied disorders of HD including both Hypo and IND (P<0.0001). The incidence of Hypo was also significantly greater than that of Hypo and IND (P<0.01, P<0.0001, respectively). Both HD and IND could be diagnosed by rectal mucosal biopsies with AChE staining. However, accurate diagnosis of Hypo could be made only through examination of the submucosal and myenteric plexuses by NADPH-diaphorase staining in full-thickness rectal specimens. CONCLUSIONS: We were able to obtain accurate diagnosis of childhood patients with HD and IND by rectal mucosal biopsy with AChE staining. On the other hand, accurate histological diagnosis in patients with Hypo could also be obtained by NADPH-diaphorase staining in full-thickness rectal specimens. That is to say, it is easier for the investigator to detect the cholinergic fiber and ganglion cell in the gut wall using NADPH-diaphorase staining than by using AChE staining.