Background: Anal fissure is a painful wound in the anoderm due to spasm of internal anal sphincter. Surgery reduces the basal sphincter tone by partial or total incision of the internal anal sphincter. In this study, we compared partial and total sphincterotomy in patients with anal fissure.Materials& Methods: In this cohort, 100 patients with anal fissure referred to the Shahid Mohammadi hospital, Bandar Abbas, Iran were randomly assigned in partial or total Sphincterotomy (50 patients in each groups) and were operated. Then the complications including, pain, bleeding during and after surgery, incontinence to the flatus or stool soiling, infection and abscess, hematoma, postoperative sphincter incontinence, anal stenosis and recurrent anal fissure within one year after operation were compared between two groups.Results: The mean age of patients was 15.28 ± 43.34 years. The rate of recurrence and incontinence to the flatus and fecal in total technique was more than partial and the amount of bleeding and hematoma, infection, abscess and discharge in total group was lower than partial, but the difference was not significant. The flatus incontinence in total group was significantly more than partial, and the level of pain in total group was significantly lower than partial.Conclusion: The results showed that partial and total sphincterotomy techniques in patients with anal fissure were comparable; however, total sphincterotomy was related to lower pain and partial sphincterotomy showed lower flatus incontinence.