A rectal fistula (also called an anal fistula or fistula-in-ano) is an abnormal tunnel that forms between the inside of the anal canal and the skin near the anus. It almost always develops after an anal abscess, a pocket of infection that drains or bursts and leaves behind a channel that won’t close on its own. The tunnel has an internal opening inside the anal canal and an external opening on the skin, and it can cause persistent drainage, pain, and recurring infections.
How a Fistula Forms
The anal canal contains eight to ten tiny glands arranged in a ring at the level of the dentate line, the boundary between the upper and lower portions of the canal. These glands sit deep in the muscular wall, penetrating the inner sphincter muscle and ending in the space between the two sphincter rings. Under normal conditions they function without issue, but when one becomes blocked, bacteria can build up and spread into the surrounding muscle tissue.
This process, known as the cryptoglandular hypothesis, explains most cases. The trapped infection forms an abscess, which is essentially a pressurized pocket of pus. The body (or a surgeon) drains the abscess, but in roughly 30 to 50 percent of cases, the drainage path doesn’t seal shut. Instead, it matures into a lined tunnel: the fistula. Because the internal opening persists, stool bacteria keep re-entering the tract, preventing it from healing.
Common Causes and Risk Factors
Most fistulas result from those infected anal glands, but several conditions raise the risk significantly. Crohn’s disease is the most notable. Nearly half of Crohn’s patients already have a perianal fistula at the time of diagnosis, and the five-year cumulative rate climbs to about 61 percent. Men with Crohn’s are affected more often than women, with rates around 68 percent versus 44 percent over five years.
Other risk factors include prior anal surgery, radiation therapy to the pelvic area, tuberculosis, sexually transmitted infections, and hidradenitis suppurativa (a chronic skin condition that causes deep, recurring abscesses in areas where skin rubs together). Trauma during childbirth can occasionally lead to a fistula as well, though this is less common.
What a Fistula Feels Like
The most common symptom is persistent or intermittent drainage from a small opening near the anus. The discharge can be pus, blood-tinged fluid, or occasionally stool. Many people notice staining on their underwear or a foul smell they can’t control with hygiene alone. Pain is typical, often described as a constant, throbbing ache that worsens when sitting, moving the bowels, or coughing. The skin around the external opening may look red and swollen.
Symptoms tend to cycle. When the tunnel becomes blocked, pressure and pain build, sometimes with fever and general malaise, mimicking a new abscess. Once the tract drains again, the pain temporarily eases. This cycle of buildup and drainage is one of the hallmarks that distinguishes a fistula from a one-time abscess.
How Fistulas Are Diagnosed
A surgeon can often identify a fistula during a physical exam by spotting the external opening and feeling for the tract underneath the skin. But imaging is frequently needed to map the full path of the tunnel, especially if it branches or dives deep through the sphincter muscles. Getting this map right matters because it determines which surgery is safe to perform.
MRI is the gold standard. Studies report that MRI identifies the internal opening of a fistula with about 98 percent sensitivity and detects the full tract with nearly 99 percent accuracy. Endoanal ultrasound, performed with a small probe inserted into the anal canal, is another option and works well in experienced hands. Your surgeon may use one or both, depending on how complex the fistula appears.
Types of Fistulas
Fistulas are classified by the path the tunnel takes through the sphincter muscles, because this determines how much muscle a surgeon would need to cut. The four main types are:
- Intersphincteric: The tunnel runs between the two sphincter muscle rings without crossing the outer one. This is the most common type and generally the simplest to treat.
- Transsphincteric: The tunnel passes through both the inner and outer sphincter muscles. Treatment is more complex because cutting through the outer sphincter can affect bowel control.
- Suprasphincteric: The tunnel travels upward between the sphincter rings, loops over the top of the outer sphincter, and then exits through the skin. This is uncommon.
- Extrasphincteric: The tunnel bypasses both sphincters entirely, often originating higher in the rectum. This is the rarest type and usually signals an underlying condition like Crohn’s disease or a complication from prior surgery.
Simple, low-lying fistulas that involve minimal muscle are treated differently from complex, high fistulas that thread through a large portion of the sphincter. The distinction between “simple” and “complex” drives almost every treatment decision.
Surgical Treatment Options
Fistulas almost never heal on their own. Surgery is the primary treatment, and the goal is to close the tunnel permanently without damaging the sphincter muscles that control bowel function.
Fistulotomy
This is the most effective procedure for simple fistulas. The surgeon cuts open the entire length of the tunnel, converting it from a tube into an open groove that heals from the bottom up. It works well when the fistula passes through only a small amount of sphincter muscle, because the risk of incontinence is lowest in those cases. For straightforward fistulas, fistulotomy has success rates above 90 percent.
Seton Placement
When the fistula passes through a significant portion of the sphincter muscle, cutting it open in one go could compromise bowel control. Instead, the surgeon threads a thin loop of material (a seton) through the tunnel. The seton keeps the tract open and draining, prevents new abscesses, and can gradually encourage the tract to migrate toward the surface over weeks or months. It’s sometimes a bridge to a more definitive repair.
LIFT Procedure
The ligation of intersphincteric fistula tract (LIFT) procedure is designed for fistulas that cross through the sphincter. The surgeon accesses the tunnel through the space between the two sphincter rings, ties off the tract, and removes it without cutting through muscle. A study of 82 patients with high transsphincteric fistulas found an overall success rate of about 80 percent. Roughly 20 percent experienced failure, with some converting to a simpler type of fistula and others developing recurrence.
Other Approaches
Several newer or less common techniques exist for complex fistulas. These include advancement flaps, where a piece of rectal tissue is used to cover the internal opening, and injectable biological plugs or pastes designed to seal the tract from within. Success rates vary and tend to be lower than fistulotomy, but these methods carry less risk to the sphincter.
Risks of Surgery
The primary concern with any fistula surgery is bowel incontinence, meaning reduced control over gas or stool. In one study of 98 patients who underwent either fistulotomy or seton placement, about 11 percent developed some degree of incontinence after surgery. Importantly, none of these cases involved permanent loss of control over solid stool. The changes were typically mild, such as occasional difficulty controlling gas.
The risk increases with the amount of sphincter muscle involved, the number of prior surgeries on the same area, and whether the patient has underlying conditions like Crohn’s disease. This is precisely why surgeons invest so much effort in imaging the tract before operating: the goal is to choose the least invasive approach that still resolves the fistula.
Recovery After Surgery
Recovery timelines depend on the procedure. After a fistulotomy, most people find that daily routines are disrupted for about two weeks. You can generally return to work within that window, though physical jobs may require a longer absence. The surgical wound itself, however, takes considerably longer to heal, often several months, because it closes gradually from the inside out.
During recovery, expect some drainage and discomfort at the wound site. Sitz baths (sitting in a few inches of warm water) help keep the area clean and ease soreness. Most surgeons recommend avoiding heavy lifting and strenuous activity for the first few months. Stool softeners or a high-fiber diet can make bowel movements less painful during healing.
Recurrence is a real possibility. Fistulas can return even after successful surgery, particularly complex ones or those associated with Crohn’s disease. Follow-up appointments allow your surgeon to check that the wound is healing properly and catch any signs of recurrence early.