Background: an inexpensive and effective method of treatment of high complex perianal fistulae is seton suture. Most difficult point in seton is maintaining tension and pressure on suture to produce muscle cutting in anal sphincters. Objective: the aim of this study was to assess the consequence, which fail to be noticed in seton suture to diminish the recurrence rate and incontinence after the treatment of fistulae. Patients and Methods: this study was conducted on 53 patients who underwent treatment for an anal fistula with staged seton suture. Clinical examination and MRI fistulogram was done to all patients. Prolene 1 was used as drainage then cutting. Follow up in outpatients was recorded. Results: there was no pain or mild pain in all cases. The recurrence rate in two cases (3.7%). Incontinence to flatus in three cases (5.6%) and one case to soft stool (1.8%). Conclusion: there were many factors affecting outcome of high perianal fistula surgery by seton suture to decrease recurrence and incontinence such as proper examination of the patient, magnetic resonance image (MRI) fistulogram, meticuolous surgery and good identification of internal opening.