Anorectal innervation that governs sensation, motor function, and rectal accommodation can be influenced by the type of surgical procedure used to treat children with Hirschsprung disease. At our institution, we began to perform single-stage, laparoscopy-assisted transanal endorectal pull-through (LATEP) with submucosal dissection and anastomosis of the ganglionated bowel at 2 different levels relative to the dentate line.This retrospective study describes postoperative stool frequency changes in response to this procedure. Forty infants who underwent single-stage LATEP between September 2003 and April 2012 in a single center by the same surgeon were included in our analysis.The patients were divided in 2 groups: Group A (n = 23) underwent submucosal dissection and anastomosis at 2 mm above the dentate line, and Group B (n = 17) underwent the same procedure with anastomosis 15 mm above the dentate line. Clinical characteristics, clinical findings on the first postoperative visit, and instances of coexisting anomalies did not differ between the 2 groups. Aganglionic segments were found in the rectosigmoid colon in 18 cases (78.2%) in Group A and in 15 cases (88.2%) in Group B. Although the stool frequency was no different at 1, 3, 6, and 12 months after the operation, Group B showed significantly fewer bowel movements than Group A after 2 years (3.77 in Group A vs 2.0 in Group B; P = 0.035) and after 3 years (3.92 vs 1.29; P = 0.009) in patients who had aganglionosis of the rectosigmoid colon. The mean follow-up period was 65.87 ± 28.08 months for Group A and 35.59 ± 18.68 for Group B.The level of submucosal dissection and anastomosis in single-stage LATEP influenced the stool frequency in rectosigmoid aganglionosis.