The aim of this study was to examine precisely the morphological abnormalities in the myenteric plexus at the atretic end of the bowel in jejunoileal atresia (JIA). Although changes in the myenteric plexus has been examined in the proximal and distal segments of bowel in JIA, a histochemical analysis of the atretic segment is lacking. Specimens from the atretic end of bowel were obtained from six neonates with JIA. Whole-mount preparations were made of the myenteric plexus, and the cholinergic and nitrergic components were studied by staining with acetylcholine esterase (Ach E) and NADPH diaphorase, respectively. Controls were obtained from two neonates undergoing small bowel resection for Meckel's diverticulum. At the blind end of bowel in type 3a atresia (5 neonates), the intensity of NADPH staining was comparable with controls. However, there was distortion of polygonal architecture of the primary and secondary plexuses at the blind end arranged in concentric fashion parallel to the circular muscle fibres. The ganglia were large and irregularly shaped and contained round neuronal cells. In the sausage shaped segment of bowel in multiple atresia, there was total loss of polygonal architecture with abnormal ganglia, and whorls of nerve fibers. Neuronal cells could not be made out in the ganglia. In specimens stained with Ach E, the findings were similar except that the staining intensity was markedly reduced compared with controls. The morphological abnormalities in the atretic bowel in type 3a were restricted to the architecture of the plexuses and ganglia. The neuronal cells were normal. However, the total loss of polygonal architecture and absence of neuronal cells in the ganglia in multiple atresia probably indicate a different etiology for this type of atresia.