Background: The aim of this study was to compare the clinical results obtained with the cutting seton and the two-stage seton fistulotomy (TSSF) in the surgical management of high anal fistula. Methods: The case records of 59 patients with high anal fistula of cryptoglandular origin treated with cutting seton (n = 12) or TSSF (n = 47) over a 5-year period were retrospectively reviewed. There was no difference between the groups in age, sex distribution, or estimated percentage of anal sphincter involved by the fistula. Follow-up was by a mailed questionnaire inquiring about fistula recurrence, incontinence, and degree of satisfaction. Mean follow-up was similar in both groups (27 months for cutting seton versus 33 months for TSSF). Comparisons were made by Student t and χ2 tests, as required. Results: There were no differences in the rate of fistula recurrence between the groups treated with cutting seton or TSSF (one of 12 versus four of 47), difficulty holding gas (six of 12 versus 25 of 47), underwear staining (six of 12 versus 18 of 47), stool incontinence (three of 12 versus 12 of 27), overall incontinence (eight of 12 versus 31 of 47) and mean incontinence score (4.9 versus 4.2). The fistula healing time and degree of satisfaction with the operation were not significantly different between the groups. One- half of the patients treated by TSSF had the seton removed under general or epidural anaesthesia. Conclusion: Both techniques are equally effective in eradicating the fistula, and both are associated with a similar rate of incontinence.