Introduction: Hirschsprung's Disease (HD) is a common congenital disease of colorectum. The initially treatment consisted of preoperative diverting colostomy, followed by definite abdominal pull-through and closure of colostomy on later date. This study was conducted to compare Trans Endo Rectal Pull Through (TERPT) and Trans Abdominal Pull Through (TAP) methods in patients with HD.Methods: 62 children (39 males and 23 females) with proven HD on the basis of rectal biopsy or barium enema underwent TAP or TERPT in one center and by unique operative team between January 2009 and August 2011. Children with a prineal disease, concomitant congenital anomaly, and total colonic agangelionosis were excluded. All patients had post operative pathologic proof.Results: 12 months follow-up showed that, the most common post operative complication in both groups was perianal excoriation (24.2%) followed by enterocolitis (22.53%), soilage (20.96%), constipation (14.50%), anal stricture (6.5%), fecal incontinency (3.2%) and anastomosis leak (3.2%). There was a significant difference between TERPT and TAP groups in operative time (107-155 min), surgical site infection (all 5 patients were in tap group), need to re-hospitalization (25%-41.5%) and cosmetic (4%-62.2%). There was no difference between age and sex of the patients and post operative complication.Conclusion: TERPT in comparison to TAP would be an alternative, safe technique for HD patients. The TERPT approach is less invasive and can provide a better clinical outcome than TAP in terms of operative time, surgical site infection need to re-hospitalization and cosmetic.