PURPOSE: This randomized clinical trial was conducted to compare a fistulectomy and a fistulotomy with marsupialization in the management of a simple anal fistula. METHODS: Forty patients with simple anal fistula were randomized into two groups. Fistulous tracts were managed by using a fistulectomy (group A) while a fistulotomy with marsupialization was performed in group B. The primary outcome measure was wound healing time while secondary outcome measures were operating time, postoperative wound size, postoperative pain, wound infection, anal incontinence, recurrence and patient satisfaction. RESULTS: Postoperative wounds in group B healed earlier in comparison to group A wounds (4.85 +/- 1.39 weeks vs. 6.75 +/- 1.83 weeks, P = 0.035). No significant differences existed between the operating times (28.00 +/- 6.35 minutes vs. 28.20 +/- 6.57 minutes, P = 0.925) and visual analogue scale scores for postoperative pain on the first postoperative day (4.05 +/- 1.47 vs. 4.50 +/- 1.32, P = 0.221) for the two groups. Postoperative wounds were larger in group A than in group B (2.07 +/- 0.1.90 cm2 vs. 1.23 +/- 0.87 cm2), however this difference did not reach statistical significance (P = 0.192). Wound discharge was observed for a significantly longer duration in group A than in group B (4.10 +/- 1.91 weeks vs. 2.75 +/- 1.71 weeks, P = 0.035). There were no differences in social and sexual activities after surgery between the patients of the two groups. No patient developed anal incontinence or recurrence during the follow-up period of twelve weeks. CONCLUSION: In comparison to a fistulectomy, a fistulotomy with marsupialization results in faster healing and a shorter duration of wound discharge without increasing the operating time.