We used Acetylcholinesterase (AchE) staining and neural cell adhesion molecule (NCAM) immunoreactivity to examine such resected lengths to determine the complete innervation profile of resected bowel in Hirschsprung's disease (HD). Resected specimens of colon obtained at pull-through surgery from 15 patients with HD [short type (S-type: n=5), recto-sigmoid type (RS-type: n=5), long type (L-type: n=5)] were sectioned at 1.5 cm intervals and stained conventionally with AchE histochemistry and NCAM immunohistochemistry. The number of positive nerve fibers (PNFs) in the lamina propria and smooth muscle layers was assessed on a scale of 0 to 3 where 0 meant no PNF and 3 meant many PNFs. The three types of HD had different AchE and NCAM innervation profiles, especially the L-type. There were also different AchE and NCAM innervation patterns seen within the same aganglionic or transitional segments of bowel depending on the site of sampling. The mean proportion of transitional segment in resected specimens from RS-type HD was significantly larger than that of S-type HD (P<0.001) although the proportion of aganglionic segments from S- and RS-type HD were almost the same. Our results suggest that the etiology of L-type HD may be different from the etiology of S- and RS-type HD because of different innervation profiles. Because segments of the excised bowel would appear to have different innervation patterns depending on whether the specimen is sampled proximally or distally, it is important to record the exact site of sampling to allow valid comparisons between types of HD to be made.