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Background One stage transanal Soave pull-through procedure (TSPP) is a recent popular operation in the treatment of Hirschsprungs disease (HD). With no visible scar and a short hospital stay, it is well accepted by surgeons and mothers. In the conventional Soave procedure, a long rectal muscular cuff left for anocolic anastomosis might increase the incidence of postoperative enterocolitis and constipation. This study presents a modified transanal Soave pull-through procedure (MTSPP) which includes an oblique mucosectomy and an oblique anastomosis with a short split muscular cuff..Methods A review of two groups of HD patients was made: 112 underwent conventional transanal Soave procedure from 1999 to 2001 (group 1) and 140 underwent modified transanal Soave procedure from 2002 to 2004 (group 2). A comparison was made between the two groups on operative data and postoperative complications. The data included: age at the operation, operating time, blood loss, time to feeds and hospital stay, occurrence of postoperative enterocolitis or constipation, need for anal dilatation, postoperative bowel function and perianal skin problems. Results There was no significant difference between two groups with respect to age, gender, length of colon resected, operating time, blood loss and hospital stay. However occurrence of postoperative enterocolitis, constipation, anastomotic stricture and time needed for anal dilatation were evidently less in group 2 (MTSPP). The mean operating time in group 1 was (106 ± 39) minutes with a range of 60 to 170 minutes; in group 2 was (101 ± 36) minutes with a range of 66 to 190 minutes. The average length of the bowel resected in group 1 was (24 ± 7) cm, range 15 to 58 cm; in group 2 was (26 ± 8) cm, range 15 to 70 cm. Two patients, one in each group, required laparoscopic assistance because of long aganglionic colon. Another patient in group 2 required laparotomy because of total colonic aganglionosis. Postoperative complications in group 1 included: temporary perianal excoriation in 34 patients (26 were