The management of fistulas largely depends on the extent of the fistula and the degree of inflammation and infection present. If a large infected fluid collection is present, this is usually drained in the operating room prior to any other intervention. Treatment with antibiotics is also common. At times, a drain called a seton is placed to keep the fluid collection from reforming. It is also important to assess both the internal and external opening of the fistula and the path of the tract between them in order to determine the best treatment option. This may be accomplished by an exam under anesthesia or other radiologic studies such as an MRI or an ultrasound study. The degree of inflammation from Crohn’s disease present in the rectum and anus must also be assessed. If inflammation is present, medical therapy is utilized first with the hopes of improving the degree of inflammation and promoting spontaneous closure of the fistula.

If there is no rectal inflammation, a surgical option may be possible. If the tract between the internal and external opening is superficial, a fistulotomy, opening of the tract, may be performed. In the case of a more complicated fistula without rectal inflammation, it may be possible to close off the internal opening with a flap of healthy rectal tissue; this is commonly done to treat a rectovaginal fistula. In many cases, however, the fistula tracts are complex and multiple and long-term use of draining setons is the preferred method of treatment. Setons are usually well tolerated and keep painful, infected fluid collections from forming. In the most severe cases of perianal fistulas and infections secondary to Crohn’s disease, a temporary or permanent ostomy, where the stool is passed out of the intestine and through the abdominal wall into a bag, is required.

The management of anal fistulas is challenging and is based upon the patient’s presentation considering the fistula’s location and complexity, the presence or absence of rectal inflammation, and the severity of accompanying anal canal disease [1]. In general, a conservative surgical approach is adopted because a more aggressive attitude often results in outcomes that are worse than the disease itself. Proper evaluation for perianal fistulas includes physical examination, an examination under general anesthesia, and possible pelvic imaging including MRI, CT scan imaging, and/or endoscopic or endorectal ultrasound imaging [2]. These techniques help define the precise extension of the disease and are needed to rule out complications such as abscesses. Adequate diagnosis has been obtained in 100 % of cases when the evaluation included pelvic MRI and examination under anesthesia or when either of these techniques was combined to endorectal ultrasounds [3]. Once the anatomy of the fistula tract and the presence or absence of rectal inflammation have been determined, appropriate therapy can be outlined.

Surgery will eventually be required in 20–80 % of Crohn’s disease patients with perianal fistulas [4–7] and about 30 % of patients with complicated perianal Crohn’s disease may eventually require a permanent stoma [8, 9]. Surgical therapy has to be tailored to each case, but the overall goal of surgery should be to cure the fistulas without damaging sphincter function. If inflammation is present, surgical therapy should be aimed at draining abscesses and placing non-cutting setons to control sepsis and prevent recurrent abscess formation. The seton does delay fistula healing and closure, but medical therapy, including immunomodulators, may be given while a seton is in place. One strategy is to place setons in patients with known fistulas who are about to start therapy with infliximab, specifically for the prevention of an abscess while on therapy [10]. Setons are well tolerated by most patients and they cause no long-term harm. Patients who have responded well to infliximab will generally have the seton removed, which can be done easily and painlessly in the physician’s office. After removal of the seton, medical therapy should be continued.

In the absence of rectal inflammation, more surgical options exist. Low perianal fistulas in patients without rectal inflammation can be treated by fistulotomy, with reported healing rates of 80 % or more. Another option is to use a rectal advancement flaps to cover the internal opening of the fistula. This technique is commonly used in the treatment of rectovaginal fistulas. In two studies, initial healing rates with advancement flaps were 71–89 %, but with recurrence rates of 34–63 % during subsequent follow-up [11–13].