Purpose In some anal fistulas, the internal/primary opening cannot be located even after examination and assessment on MRI or transrectal ultrasound. The efficacy of a simple new protocol to manage such therapeutically challenging fistulas was tested. Patients and methods All anal fistula patients operated consecutively over 7 years were included in the study. A simple two-step protocol was followed for fistulas in which the internal opening was not locatable after clinical examination and MRI assessment. First, the MRI was reassessed. The site where the fistula was closest to the internal sphincter was noted. It was assumed that the was located at that position and the fistula was treated accordingly. Second, in horseshoe anal fistulas with no apparent internal opening, it was assumed that the internal opening was located in the midline. Low fistulas were treated by fistulotomy and high fistulas by a sphincter-sparing procedure. Incontinence was evaluated by objective incontinence scores (Vaizey scores). Results A total of 757 patients were operated (median follow-up-33 months). Of these, 57 patients were excluded due to short or inadequate follow-up. In 154/700 (22%) patients, the internal opening could not be located while in 546/700 (78%), the internal opening was found. Both the groups were similar in all parameters. In the internal-opening group, the fistula healed completely in 486/546 (89%) and in the 'internal-opening not found group', the fistula healed in 140/156 (90.9%) (p=1.01). The objective continence scores did not change significantly after surgery in both the groups. Conclusion This new protocol seems effective as a high cure rate could be achieved in 'internal-opening not found' fistulas which was comparable to fistula healing in the 'internal-opening found' group.