Over the years from 1992 to 1997, 41 anorectal malformations (ARM) with histopathologic alterations were investigated to determine which morphologic abnormalities of the distal rectum accompany ARMs. Three other cases showed normal neuromuscular morphology; 9 further cases could not be evaluated owing to scanty biopsies. All resected specimens were caudocranially coiled and cryostat cut at -20 degrees C into serial sections, which were stained with a lactic dehydrogenase, succinic dehydrogenase, nitroxide synthase, and acetylcholinesterase reaction as well as hemalum and sirius red. Ten low, 15 intermediate, and 10 high forms of anal atresia (AA) were studied. In addition, six cloacal abnormalities were investigated. In 7 cases (17%) (5 intermediate, 2 low AAs), the characteristics of Hirschsprung's disease were observed. Oligoneuronal hypoganglionosis of the myenteric plexus proximal to the anal floor was diagnosed in 7 AAs (12%). In 10 children with high-type AA and resection of 1-5 cm distal rectum and in all cloacal anomalies (n = 6) defects of the muscularis propria were seen in the rectal-atresia sac. These defects were characterized by hypoplasia of the circular-muscle layer and/or the internal anal sphincter (IAS). Intestinal neuronal dysplasia of the submucous plexus was most frequently observed (12%) in high-type AA. A correlation between innervation anomalies or anomalies of the muscularis propria and the type of fistula could not be seen. In conclusion, all cases with high-type AA and cloacal anomalies were characterized by anomalies of the muscularis propria and/or IAS but this was not the case in intermediate and low-type AAs. Anomalies of the enteric nervous system were diagnosed in 60% of AAs.