We investigated enteric innervations in 15 isolated and five syndromic cases of Hirschsprung disease (HSCR) with immunohistochemistry for the S100 protein (S100), class III α-tubulin (TUJ1), peripherin, neuronal nitric oxide synthase (nNOS) and CD34. The number of neurites per smooth muscle unit of the circular muscle layer (CML) was counted in the longitudinal sections. TUJ1 was the best marker to detect whole neuritic networks of the enteric nervous system. There were differences in the innervation patterns between isolated rectosigmoid aganglionosis (RS) and long segment aganglionosis (LS) including total colonic aganglionosis and extensive aganglionosis. In the aganglionic bowel (AGB) of LS, no nerve fibers innervated smooth muscle units in the CML in the area from the small bowel to the terminal descending colon. In the rectosigmoid region of every type of isolated HSCR, we observed transmural nerve fibers forming meshworks in the CML with TUJ1 and S100 antibodies. In RS, the neurites running parallel with smooth muscle cells gradually decreased in number in the distal portion. However, in the rectosigmoid AGB in LS, those neurites were absent and most neurites perpendicularly crossed the CML. Hypertrophic nerve trunks (HNT) in the submucous and myenteric plexuses were observed more frequently in the rectosigmoid region than in the rostral portion. Based on these data, it is suggested that the neuritic meshworks in the CML of the rectosigmoid AGB might derive from not only the sacral plexus, via HNT, but also intrinsic neurons in the oligoganglionic bowel. All of the syndromic HSCR were RS. In the AGB of RS with Down syndrome, the distribution of neurite meshworks in the CML is markedly reduced. In the AGB of RS with mental retardation suspected of having Mowat–Wilson syndrome, the density of intramuscular innervation was comparatively higher. In the rostral portion to the AGB of syndromic HSCR, myenteric ganglia were clearly small in size, and more numerous per smooth muscle unit with scarce internodal strands. These dysplastic features fall under neither hyperganglionosis nor hypoganglionosis classifications. We considered that syndromic HSCR might occur on the basis of a dysplastic enteric nervous system caused by genetic alteration.