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The treatment of high anal fistula using endorectal advancement flaps represents an important technique to attain cure of fistulation and preserve anal continence. The creation of the advancement flap may comprise the rectal mucosa only or involve the full transection of the rectal wall. A comparison between full-thickness flaps and mucosal (partial-thickness) flaps was made to analyze the defining elements of successful fistula treatment: recurrence rates and anal continence.A retrospective review of 54 consecutive patients with high anal fistula of cryptoglandular origin was undertaken. Patient risk was categorized according to previous anal surgery. Continence was assessed according to the Vaizey score. Recurrence rates were recorded in a long-term, complete follow-up.Thirty-four patients underwent surgery using a partial-thickness flap; in 20 patients the full-thickness flap was used. There were no major intraoperative or postoperative complications. Continence scores revealed significant incontinence in 11.1 percent of all patients. Full transection of the rectal wall for flap creation did not pose a threat to continence. Twenty-four percent of all patients suffered from a recurrence. Patients with four or more previous anal surgeries were at highest risk for failure. A single patient in the full-thickness flap group (5 percent) as opposed to 12 patients (35.3 percent) in the partial-thickness group suffered from recurrence.The comparison of partial-thickness to full-thickness endorectal advancement flaps suggests an improvement of recurrence rates without higher incontinence rates when a full mobilization of the rectal wall is performed.