Hirschsprung disease, which consists of aganglionosis of the rectum and sometimes more proximal bowel, requires surgical removal of the aganglionic bowel and creation of ganglionated neorectum using proximal normally innervated bowel. The border between aganglionic and ganglionic bowel is irregular; the transition zone features variable quantities of ganglion cells and numerous large nerves. We report the histopathology of pull-through bowel segments resected because of poor postoperative outcome from 30 patients (22 boys, 8 girls). The most common indication for reoperation was severe constipation/obstruction. Transition zone (bowel with at least two nerves ≥40 µm diameter per 400× high-power field, and ganglion cells) or aganglionic bowel (bowel with at least two nerves ≥40 µm per high-power field diameter, but without ganglion cells) was found in 19/30 (63%) resections. In colons resected because of familial adenomatous polyposis, rare high-power fields showed two enlarged nerves; the mean age of those patients (135 ± 49.4 months) was significantly higher than that of the patients undergoing redo pull-through surgery (67.9 ± 42.8 months). Additional pathology included stricture and enterocolitis. Although there are multiple causes for poor outcomes following surgical therapy for Hirschsprung disease, abnormal innervation of the bowel used for pull-through is common. We recommend that intraoperative consultation at primary pull-through procedure include frozen section evaluation of the circumference of the bowel to be used for pull-through to confirm histologically the presence of both ganglion cells and normal-caliber nerves. The criteria used in this study are most suitable for infants and young children.