To determine the long term outcome of cutting seton fistulotomy.An audit of fistula surgery using a cutting seton for cryptoglandular sepsis identified 32 patients treated between 1988-1996. The majority of the patients had a trans-sphincteric (26/32, 81%) fistula.Fourteen (44%) had had previous fistula surgery before seton fistulotomy. Follow up was complete in 28 patients: 8 patients had recurrence (29%), 4 at a new site and 4 at the same site after apparent healing. Major incontinence was reported by 3 patients, minor incontinence by 7 and soiling by 5, but only 7 patients worsened after the cutting seton fistulotomy. Major incontinence was reported only by women who had a previous vaginal delivery.Cutting setons do not always preserve continence in high trans-sphincteric and complex fistulas. Patients should be warned about a high recurrence rate after cutting seton fistulotomy. The use of a cutting seton for anterior fistulas in female patients with a history of vaginal delivery should be avoided because of the risk of incontinence.