A fistula is an abnormal tunnel that forms between two body surfaces, and it’s one of the most common complications of Crohn’s disease. Up to 50% of people with Crohn’s will develop at least one fistula during their lifetime. These tunnels can connect the intestine to the skin, the bladder, the vagina, or another section of the bowel, and they form because Crohn’s inflammation doesn’t stay on the surface. It burrows through the full thickness of the intestinal wall.
How Fistulas Form
Crohn’s disease causes inflammation that penetrates all layers of the bowel wall, not just the inner lining. Over time, this deep inflammation creates small channels called sinus tracts that bore outward. When a tract breaks through the outer wall of the intestine and reaches another organ or the skin surface, it becomes a fistula.
At a cellular level, the intestinal lining cells undergo a transformation where they take on properties of connective tissue cells. This makes them more mobile and invasive. The body also ramps up production of enzymes that break down the structural tissue between organs, essentially clearing a path for the tunnel to extend. This is why fistulas tend to develop in people with long-standing or poorly controlled Crohn’s rather than appearing early in the disease.
Types of Fistulas and Their Symptoms
Fistulas are named based on where they start and where they end up. The symptoms you experience depend entirely on which structures the tunnel connects.
Perianal fistulas are the most common type. These run from the anal canal to the skin near the anus. You might notice drainage of pus or mucus, pain around the anus, swelling, and occasionally bleeding. They can significantly affect quality of life, including sexual function.
Enterocutaneous fistulas connect the intestine to the skin surface, usually on the abdomen. Intestinal contents leak through to the skin, which can cause skin breakdown and irritation. These carry serious risks: sepsis and malnutrition are the leading causes of death in these cases, occurring in 10% to 30% of patients.
Entero-enteric fistulas connect two sections of the small intestine. These are often asymptomatic since intestinal contents are simply passing between two parts of the same system, though they can cause abdominal pain and fever.
Enterovesical fistulas tunnel from the intestine into the bladder. The hallmark symptoms are painful urination and pneumaturia, which is the passage of air in your urine. This happens because gas from the intestine travels through the tunnel into the bladder.
Rectovaginal fistulas connect the rectum to the vagina, leading to recurrent vaginal infections and pain during intercourse.
Gastrocolic fistulas connect the colon to the stomach and can cause a distinctive symptom: belching that tastes fecal. They also cause diarrhea, weight loss, and bacterial overgrowth in the small intestine. Surgery is typically the primary treatment for these.
How Fistulas Are Diagnosed
Pelvic MRI is the first-line imaging method for detecting and mapping fistulas, particularly perianal ones. A European expert panel rated MRI as the strongly preferred modality because of its proven diagnostic benefit and the highest level of supporting evidence. MRI is especially valuable for complex fistulas with multiple branches or deep extensions, which are common in Crohn’s.
Endoanal ultrasound (a small probe inserted into the anal canal) performs comparably to MRI for simple, straightforward fistulas. But because Crohn’s fistulas tend to be complex, MRI remains the standard. Ultrasound is primarily reserved for patients who can’t undergo MRI. When surgery is planned, MRI is particularly useful for mapping the exact course of the fistula tract so the surgeon knows what they’re dealing with.
Abscess Formation
Fistulas and abscesses often go hand in hand. The fistula tract can become blocked, trapping infectious material and forming a painful, swollen abscess. Treatment typically involves draining the abscess using a needle guided by CT imaging, along with antibiotics. However, when an abscess is connected to a fistula, drainage alone frequently fails. If the drain continues producing more than about 20 milliliters per day of thick fluid, imaging usually reveals that the abscess is being fed by a fistula connection to the bowel, and surgery becomes necessary.
Treatment With Medication
Biologic medications that block a protein called TNF-alpha are a cornerstone of fistula treatment. The landmark ACCENT II trial found that 36% of patients treated with a TNF-blocker achieved fistula closure, compared to 19% on placebo. For rectovaginal fistulas specifically, about 45% of patients achieved closure within 14 weeks of starting treatment. Patients who responded and continued on maintenance therapy kept their fistulas closed for a median of 46 weeks, compared to 33 weeks for those switched to placebo.
A systematic review of 137 patients with Crohn’s-related rectovaginal fistulas found that medication alone cured about 38% of cases. Combining medical therapy with surgery raised that to roughly 44%. These numbers reflect the reality that fistulas are among the most stubborn complications of Crohn’s, and complete healing is achievable but not guaranteed.
Surgical Options
For perianal fistulas, three standard approaches exist: chronic seton drainage, biologic therapy alone, or surgical closure after a short course of biologic therapy.
A seton is a thin thread or rubber band that a surgeon threads through the fistula tract and leaves in place, sometimes for a year or longer. It sounds counterintuitive, but keeping the tract open on purpose prevents it from sealing over and trapping infection inside. This avoids the cycle of abscess formation and recurrence that makes fistulas so frustrating. The seton keeps the tunnel draining freely while the underlying Crohn’s inflammation is brought under control with medication.
Surgical closure involves procedures to seal the fistula tract after biologic therapy has calmed the surrounding inflammation. This approach attempts a definitive fix but carries a risk of recurrence, particularly if the Crohn’s disease flares again.
Stem Cell Therapy
An injectable therapy using donor stem cells derived from fat tissue was approved in Europe in 2018 for complex perianal fistulas that hadn’t responded to standard treatments. In its pivotal trial, 53% of patients achieved remission at 24 weeks, compared to 36% on placebo. Real-world data from Spain showed even higher rates, with about 69% achieving remission at 6 months and no treatment-related side effects reported.
However, a larger follow-up trial failed to show a statistically significant benefit over placebo, and the manufacturer voluntarily withdrew the product from the market in January 2025. This leaves a gap in treatment options for patients with fistulas that don’t respond to biologics or surgery, and it illustrates how difficult fistula healing remains even with advanced therapies.
Living With a Crohn’s Fistula
Fistulas are not a one-time problem. They tend to recur, and managing them often means years of treatment adjustments. The location of the fistula largely determines how much it affects daily life. A small entero-enteric fistula might cause no symptoms at all, while a perianal fistula can make sitting, exercising, and intimacy painful. Enterocutaneous fistulas require careful wound management to protect the surrounding skin from digestive fluids.
Nutrition matters more than many patients realize. Fistulas can cause malnutrition by diverting food away from the absorptive parts of the intestine, and the chronic inflammation itself increases caloric needs. Weight loss and protein deficiency are common, particularly with ileocolic fistulas connecting the small intestine to the colon. Working with a dietitian familiar with inflammatory bowel disease can help prevent nutritional deficits from compounding the problem.