Background One stage transanal Soave pull-through procedure (TSPP) is a recent popular operation in the treatment of Hirschsprung’s 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 <3 months of age), enterocolitis in 21, anastomotic stricture in 11, recurrent constipation in 12, cuff abscess in 1, anastomosis leak in 1, soiling in 3 and rectal prolapse in 1. In group 2 post operative complications included: transient perianal excoriation in 37 patients (30 were <3 months of age), enterocolitis in 13, anastomotic stricture in 5, recurrent constipation in 6, anastomotic leak in 1, adhesive bowel obstruction in 1 and soiling in 4. Complete bowel continence was found in 97 children (86.6%) in group 1 and in 129 children (92.1%) in group 2 at one year followup after operation. Conclusions Modified transanal Soave pull-through procedure for HD with oblique mucosectomy and anastomosis and a short split muscular cuff is a safe and feasible operation with low incidence of postoperative complication. It is an encouraging improvement of the conventional transanal Soave pull-through procedure. MTSPP is a preferable choice in the surgery of HD. Background One stage transanal Soave pull-through procedure (TSPP) is a recent popular operation in the treatment of Hirschsprung’s 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 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 hospit al 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 The 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 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; 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 gr oup 1included: temporary perianal excoriation in 34 patients (26 were <3 months of age), enterocolitis in 21, anastomotic stricture in 11, recurrent constipation in 12, cuff abscess in 1, anastomosis leak in 1, soiling in 3 and rectal prolapse in 1 . In group 2 post operative complications included: transient perianal excoriation in 37 patients (30 months <3 months of age), enterocolitis in 13, anastomotic stricture in 5, recurrent constipation in 6, anastomotic leak in 1, adhesive bowel obstruction in 1 and soiling in 4. Complete bowel continence was found in 97 children (86.6%) in group 1 and in 129 children (92.1%) in group 2 at one year followup after operation. Conclusions Modified transanal Soave pull-through procedure for HD with oblique mucosectomy and anastomosis and a short split muscular cuff is a safe and feasible operation with low incidence of postoperative complication. It is an encouraging improvement of the conventional transanal Soave pull-through procedure. MTSPP is a prefer able choice in the surgery of HD.