Background Ligation of the intersphincteric tract (LIFT), a novel sphincter-saving technique, has been recently described with promising results. Literature data are still scant. In this prospective observational study, we present our experience with this technique. Methods Between October 2010 and April 2011, 18 patients with 'complex' fistulas underwent LIFT. All patients were enrolled in the study after a physical examination including digital examination and proctoscopy. For the purpose of this pilot study, fistulas were classified as complex if any of the following conditions were present: tract crossing more than 30% of the external sphincter, anterior fistula in a woman, recurrent fistula or pre-existing incontinence. Endpoints were healing time, presence of recurrence, faecal incontinence and surgical complications. Results Ten patients were men and 8 were women; mean age was 39 years; minimum follow-up was 4 months. Three patients required drainage seton insertion and delayed LIFT. After LIFT, 1 patient experienced haemorrhoidal thrombosis. At the end of the follow-up, 15 patients (83%) healed with no recurrence. Three patients had persistent symptoms and required further surgical treatment. We did not observe postoperative worsening of continence. Conclusions Results from our pilot study indicate that this novel sphincter-saving approach is effective and safe for treating complex anal fistula.