Single-stage transanal endorectal pull-through (TEPT) procedure is now widely used for rectosigmoid Hirschsprung's disease (HD). However, this procedure is associated with some common complications like stricture, enterocolitis, constipation, anastomotic dehiscence and perianal excoriation. The aim of this study was to evaluate the clinical outcomes of a modified TEPT operation in the management of rectosigmoid HD. 45 patients with rectosigmoid HD admitted between August, 2004 and July, 2008 were included in this study. Pre-operative barium enema was done in all of them. Patients in whom the transition zone was well delineated were included in the study. Frozen section biopsy was done to confirm the presence of ganglion cells in the pull-through bowel. All odd number patients were included in group A, where conventional TEPT procedure was performed. All even number patients and the last five patients of the series were in group B. In this group, a modified transanal endorectal procedure was done. The initial part of submucosal dissection and mobilization of aganglionic rectum was the same as in the conventional procedure. The anorectal mucosa was anastomosed end-to-side to the seromuscular coat of the ganglionic bowel. Mobilized bowel was divided at about 2 cm distal to the anastomosis. Six hitching stitches were applied from the free edge of the bowel to the perianal skin so that the anastomosis remains outside the anal verge. The distal redundant bowel was excised on eighth post-operative day. Pre-operative bowel preparation was done in all patients in group A. The bowel preparation was not mandatory in group B patients. Post-operative results of both these groups were compared and analyzed using the Mann-Whitney U test. Mean operative time in group A was 86 min (range 75-95 min) versus 90 min (range 70-100 min) in group B. Average length of the bowel resected was 20 cm (range 10-26 cm) in group A and 22 cm (12-40 cm) in group B. Post-operative feeding was started after 48 h in group A and after 6 h in group B. Average hospital stay was about 8 days in both the groups. Median follow-up was 36 months in group A (range 14-54 months) and 32 months (range 12-52 months) in group B. Anastomotic stricture or stenosis was noted in two patients in group A and none in group B (p < 0.01). Partial anastomotic dehiscence was noted in two patients in group A and none in group B (p < 0.01). Average bowel movement in group A was 6-8 per day at 1 month and 2-6 per day at 6 months. In group B, it was 8-10 at 1 month and 2-8 at 6 months. Cuff narrowing causing constipation was noted in two patients in group A and none in group B (p < 0.01). Enterocolitis following pull-through was noted in two patients in group A and three patients in group B. Four patients in group A and one patient in group B had post-operative constipation. All of them responded to bowel management program: only one of them (group A) required enema; soiling was noted in one patient each in both the groups. Modified TEPT procedure is associated with excellent clinical outcome with fewer complications, and permits early post-operative feeding. Operating time, hospital stay and post-operative bowel movement were comparable with the conventional technique.