There are many clinical conditions that resemble Hirschsprung's disease despite the presence of ganglia cells on rectal biopsy. This group has focused its research interest into delineating variant Hirschsprung's disease based on specific histochemical, immunohistochemical, silver staining and electron microscopic studies. Between 1981 and 1996, full thickness rectal biopsy or resected surgical specimens from 66 patients with clinical symptoms suggesting Hirschsprung's disease were examined. Various functional bowel disorders diagnosed using different histological techniques included, intestinal neuronal dysplasia in 23, hypoganglionosis in 6, immature ganglia in 4, absence of argyrophil plexus in 3, internal sphincter achalasia in 15, and smooth muscle disorders in 15. The findings suggest the following: (1) Clinical conditions resembling Hirschsprung's disease despite the presence of ganglia cells on suction rectal biopsy can be diagnosed by providing an adequate biopsy and employing a variety of histological techniques. (2) Intestinal neuronal dysplasia (IND) is a distinct clinical entity that can be clearly proven histologically. Patients with IND not only have abnormalities of submucosal and myenteric plexuses but also defective innervation of the muscle and neuromuscular junction as well as the internal sphincter. (3) Internal sphincter achalasia, which is histologically characterized by nitregeric nerve depletion, can be diagnosed on anorectal manometry and successfully treated by internal sphincter myectomy. (4) The outcome of smooth muscle disorders is generally fatal. The need for surgical intervention should be weighed carefully and individualized because most operations have not been helpful and are probably not necessary.