Introduction:Due to the high prevalence of anal fistulas and the recurrence of the disease following surgery, different methods have been suggested for appropriate treatment of this disease. In this study, the effects of rectal advancement flap surgery and seton placement on the recurrence rate, incontinence and wound infection were compared.Methods:In this interventional, prospective and quasi-experimental study, 45 patients with anal fistulas including 28 males and 17 females were studied for 2 years (2015-2017). Patients were divided into two groups and mucosal advancement flap and seton placement techniques were used for each of them. Descriptive analysis of data was performed by SPSS software.Results:24 patients (54%) had seton placement surgery and 21 patients (46%) underwent rectal advancement flap surgery. Recurrence was significantly higher in patients who underwent seton placement surgery than the group that underwent rectal advancement flap surgery. Twelve patients (57%) who underwent rectal advancement flap surgery showed improvement in sphincter tone while 11 patients (45%) showed improvements with seton placement.Conclusion:The overall results of this study showed that rectal advancement flap surgery reduces recurrence and wound infection more significantly than seton placement in patients with anal fistula.