This study was conducted to investigate the pathological changes which occur in interstitial cells of Cajal (ICCs) and ganglion cells found in segments of resected bowel obtained from patients with Hirschsprung's disease (HD), as well as to explore the benefits of using a contrast enema (CE) with 24-h delayed X-ray films to predict the length of resected bowel. We performed a retrospective analysis of 58 children with HD who had undergone the pull-through procedure. After each operation, the ICCs and ganglion cells present in the proximal ends of the barium residue (Level A) and resected proximal bowel segment (Level B) were analyzed using immunohistochemical staining methods. Each patient was followed up for 1 year to record their stool frequency, defecation control ability, and post-surgical complications which may have occurred. Immunohistochemical staining detected fewer ICCs in Level A than in Level B (p < 0.05). However, the density of ganglion cells in the two levels was not significantly different (p > 0.05). One patient had anastomotic stricture, and five patients suffered from enterocolitis. The density of ICCs was significantly lower in the bowel segments that displayed barium retention. A CE may be a valuable tool for predicting the length of bowel resection in patients with HD.