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Purpose: The management of complex anal fistulas remains a challenge, mainly due to the considerable risk of incontinence. We compared LIFT and VAAFT in the treatment of complex anal fistulas in terms of healing time, recurrence, continence, morbidity, and postoperative pain, focusing also on patients with local abscess at the time of surgery. Methods: We include all patients with high trans-sphincteric anal fistula even with abscess at the time of surgery. Anorectal manometry, endoanal ultrasound, Cleveland Clinic fecal incontinence score, VAS score, and number of previous fistula treatment were recorded. The clinical examination defined healing, insufficiency or recurrence of the fistula. Results: Fifty-four consecutive patients are undergoing surgery: 26 patients underwent LIFT and 28 underwent VAAFT. During the 18 months of follow-up there were no differences in terms of AM, CCFIS and VAS scores. Days of healing, failure, and recurrence rate were comparable in both groups. The subgroup of patients with local abscess undergoing LIFT showed worse results in terms of failure and recurrence rate (p < 0.05). Conclusions: Both techniques are safe and effective and can offer long-term benefits. LIFT should not be used as a first treatment in high trans-sphincteric fistula with perianal abscess. [ABSTRACT FROM AUTHOR]