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Transanal advancement flap repair is successful in 2 of every 3 patients with a cryptoglandular fistula passing through the middle or upper third of the external anal sphincter. It has been suggested that ongoing disease in the remaining fistula tract contributes to failure. Ligation of the intersphincteric fistula tract might be a useful tool to eradicate this ongoing disease.The aim of the present study was to evaluate the effect of an additional ligation of the fistula tract on the outcome of transanal advancement flap repair.This investigation was designed as a prospective clinical study.The study took place in a university hospital.A consecutive series of 41 patients with a high transsphincteric fistula of cryptoglandular origin were included.Ligation of the intersphincteric fistula tract was performed in addition to flap repair.Early and late complications were recorded. Continence scores were determined with the use of the Fecal Incontinence Severity Index.Median duration of follow-up was 15 months. Primary healing was observed in 21 patients (51%). Of the 20 patients with a failure, the original transsphincteric fistula persisted in 12 patients. In 8 patients, the transsphincteric fistula was converted into an intersphincteric fistula. These patients underwent subsequent fistulectomy, which was successful in all of them. The overall healing rate was 71%.This was a preliminary observational study with no control group.The ligation of the intersphincteric fistula tract procedure is prone to infection and does not enhance the outcome of flap repair.