There are a number of conditions that clinically resemble Hirschsprung's disease despite the presence of ganglion cells on rectal biopsies. These conditions have been described under various names. There have been no systematic studies to date to distinguish these conditions from one another. We examined biopsy and surgical specimens from 19 cases of allied functional bowel disorders in an attempt to establish the most appropriate diagnostic procedure. Suction rectal biopsy and full thickness surgical biopsy specimens were examined by enzyme histochemistry (AChE), immunocytochemistry (monoclonal antibody D7), silver impregnation, and electronmicroscopy. Monoclonal antibody D7, which was produced in our own laboratory, is a good marker of autonomic nervous system. This unique antibody allowed us to distinguish various neuronal abnormalities of the bowel except the abnormalities of the argyrophil plexus, which were diagnosed by silver staining. Eight of the 19 cases had a smooth muscle disorder that was only diagnosed on electronmicroscopy. Our data suggest that the vast majority of allied functional bowel disorders can be diagnosed by examining a full thickness rectal biopsy by immunocytochemistry (D7 monoclonal antibody), silver impregnation, and electronmicroscopy.