Background: In this study, we determined the long-term outcome of perianal fistulas treated with mucosal advancement flap (MF) or fistulotomy (FT). Methods: One hundred three patients with perianal fistulas were treated by MF for high fistulas or FT for low fistulas and were retrospectively assessed by case-note review and examined at the out-patient clinic. The localization and time of recurrence of the fistula were recorded. Results: Forty-one patients [median follow-up of 72 months (range 48-99)] were treated by an MF, and 62 patients [median follow up of 75 months (range 48-99)] were treated by FT. After 12, 48, and 72 months, the fistula had recurred in 9 (22%), 26 (63%), and 26 (63%) patients of the MF group and in 4 (7%), 16 (26%), and 24 (39%) patients of the FT group, respectively. Eighteen (69%) of the recurrences in the MF group and ten (33%) of the FT group occurred within 24 months after surgery (p=0.01). Four (15%) of the recurrences in the MF group and 13 (54%) of the recurrences in the FT group were present in a different localization (p=0.007). Conclusion: The success rate of both FT and MF techniques decreases with time. Recurrence appears to be caused by failure of treatment and by recurrent patient disease.