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Low fistula-in-ano has traditionally been treated with fistulectomy and fistulotomy. Recent studies have shown that marsupialisation of the fistulotomy wounds can reduce the healing time. A randomized clinical trial was conducted at Bugando Medical Centre in north-western Tanzania between January 2008 and December 2012 to compare the efficacy of fistulectomy versus fistulotomy with marsupialisation in the treatment of low fistula in ano. Patients were randomized into two groups, namely Group A (fistulectomy) and Group B (fistulotomy with marsupialisation). A total of 162 patients were enrolled in the study and randomly assigned to Group A (n= 82) and Group B (n = 80). Both groups were comparable with respect to age, sex ratio, duration of symptoms, type of fistula and radial distance of the external opening from the anal verge. The mean healing time was statistically significantly longer in group A than in group B (P = 0.002). The duration of postoperative wound discharge was statistically significantly shorter in group B than in group A (P = 0.012). There was no statistically significant difference in the mean operating time, mean operation wound size, mean postoperative pain score, rate of surgical site infection and postoperative hospital stay between the two groups (P >0.05). None of the patients in either group had recurrence or was found to have anal incontinence. No differences in the extent of adverse effects of surgery on the physical, social and sexual lives of the patients in the two groups. We conclude that in comparison to a fistulectomy, a fistulotomy with marsupialisation results in faster wound healing and a shorter duration of wound discharge and should therefore be recommended as a standard surgical procedure in the treatment of low fistula-in-ano.