Most rectal fistulas start with an infected gland inside the anal canal. The infection creates an abscess, and when that abscess drains (on its own or with medical help), it can leave behind a tunnel connecting the inside of the rectum or anal canal to the skin near the anus. Roughly one in three perianal abscesses eventually leads to a fistula, making this abscess-to-fistula progression the single most common cause.
But infected glands aren’t the only path. Crohn’s disease, childbirth injuries, radiation therapy, certain infections, and even smoking can all play a role. Here’s how each one works.
Infected Anal Glands: The Most Common Cause
The inside of the anal canal contains small glands that sit between the two rings of muscle (sphincters) controlling your bowel movements. These glands open into tiny pockets called crypts along the inner lining of the canal. Normally, they drain without issue. Problems start when one of those gland openings gets blocked.
Once blocked, bacteria from stool begin multiplying inside the trapped gland. The infection spreads along the path of least resistance, usually downward through the muscle layers, forming a pocket of pus: a perianal abscess. You’d feel this as a painful, swollen lump near the anus, often with fever. The abscess needs to be drained, but even after drainage, the original infected gland can keep leaking bacteria into the surrounding tissue. Over weeks or months, that persistent low-grade infection carves out a permanent channel from the anal canal to the skin surface. That channel is the fistula.
This process, called the cryptoglandular theory, was first described by surgeon Alan Parks in 1961 and remains the accepted explanation for the majority of cases. Studies consistently find that about 31% to 34% of patients who have an abscess drained will go on to develop a fistula afterward. In some cases, the fistula is already present at the time the abscess is discovered.
How Crohn’s Disease Creates Fistulas
Crohn’s disease is the second most important cause. Up to 50% of people with Crohn’s will develop a fistula at some point in their lifetime, and the perianal area is one of the most common locations. The mechanism is different from a simple gland infection. Crohn’s causes deep, transmural inflammation, meaning the immune system attacks through the full thickness of the intestinal wall rather than just the surface lining. That deep inflammation can bore tunnels through tissue the same way an abscess does, but it tends to create more complex fistulas with multiple branches or openings.
Perianal fistulas in Crohn’s disease are notoriously difficult to treat because the underlying inflammation keeps fueling new tunnel formation even after surgical repair. For someone with Crohn’s, a fistula around the anus is sometimes the very first symptom that leads to a diagnosis.
Childbirth Injuries
Vaginal delivery can cause tears in the perineum (the tissue between the vagina and anus) that extend deep enough to involve the rectum or the anal sphincter muscles. If those tears don’t heal properly, or if a surgical cut made during delivery (episiotomy) becomes infected, a tunnel can form between the rectum and the vagina or the rectum and the perineal skin. Delivery-related injuries are the most common cause of rectovaginal fistulas specifically. These fistulas may not become apparent until weeks after delivery, once healing stalls and an abnormal passage establishes itself.
Radiation Therapy and Cancer
Pelvic radiation, used to treat cancers of the rectum, cervix, prostate, or bladder, damages the blood supply to surrounding tissues. Over time, that radiation-weakened tissue can break down and form abnormal connections between organs or between the rectum and skin. A radiation-related fistula can appear at any point after treatment but most commonly develops within the first two years. Cancerous tumors themselves can also erode through the rectal wall and create fistulas as they grow into neighboring structures.
Infections Beyond the Anal Glands
Several specific infections can cause fistulas independently of the typical gland-blockage process. Tuberculosis can affect the perianal area, particularly in regions where TB is common, creating fistulas that look unusual on imaging and don’t respond to standard surgical approaches. Lymphogranuloma venereum (LGV), a sexually transmitted infection caused by certain strains of chlamydia, can cause invasive inflammation in the rectum. If untreated, LGV proctocolitis leads to chronic colorectal fistulas and narrowing of the rectal passage. Actinomycosis, a rare bacterial infection, can also produce fistula-like draining tracts in the perianal region.
Fistulas in Infants
Perianal fistulas in babies follow a distinct pattern. They occur almost exclusively in male infants, typically under one year of age, and are strongly linked to abnormally deep or wide anal crypts that appear to be present from birth. In one study, 92% of infant fistulas were preceded by a perianal abscess, and when doctors examined the anal canal closely, nearly half of infants had unusually deep, thick-walled crypts that made infection more likely. This suggests a congenital structural factor rather than the acquired gland blockage seen in adults. Many infant fistulas resolve on their own or with minor treatment, though the recurrence rate can be high because of the underlying crypt abnormality.
Smoking and Other Risk Factors
Smoking significantly raises the risk of developing a perianal abscess or fistula. A study of a Chinese population found that smokers had roughly 12 times the odds of developing an abscess or fistula compared to non-smokers. The likely mechanisms include impaired blood flow to the tissues around the anus, reduced immune function in the local area, and slower wound healing, all of which make it easier for a minor gland infection to progress into an abscess and then a chronic fistula. Diabetes also increases risk, likely through similar pathways of impaired healing and immune suppression. Smoking cessation is one of the few modifiable steps that can reduce both the initial risk and the chance of recurrence after treatment.
Types of Fistulas Based on Location
Not all fistulas are the same, and where the tunnel runs relative to the sphincter muscles determines both the complexity of treatment and the risk of complications. The Parks classification breaks fistulas into four types:
- Intersphincteric (45% of cases): The tunnel passes through the inner sphincter muscle but not the outer one. These are the most common and generally the simplest to treat.
- Transsphincteric (30%): The tunnel passes through both sphincter muscles. Treatment requires more care to avoid damaging the muscles that control bowel continence.
- Suprasphincteric (20%): The tunnel goes upward between the two sphincter muscles, arches over the top of the outer sphincter, and then comes back down to the skin. This category includes horseshoe-shaped abscesses that wrap around the anus.
- Extrasphincteric (5%): The tunnel connects the rectum to the skin while bypassing both sphincter muscles entirely. These are rare and often caused by Crohn’s disease, trauma, or a complication from prior surgery rather than a simple gland infection.
How Fistulas Are Identified
A physical exam is often enough to identify a fistula, particularly when there’s a visible opening on the skin near the anus that’s draining pus, blood, or stool. You might also notice persistent pain around the anus that worsens with sitting or bowel movements, redness or swelling near the opening, and occasionally fever if there’s active infection.
Imaging isn’t always necessary for straightforward cases, but when a fistula is complex or related to Crohn’s disease, MRI is the preferred tool because it can map the tunnel’s path through the soft tissues. Endoanal ultrasound, a small probe placed inside the anal canal, agrees with surgical findings in 73% to 100% of cases and is another reliable option. For complicated fistulas, combining two of these methods (MRI plus ultrasound, or either one plus an exam under anesthesia) achieves nearly 100% accuracy in mapping the fistula’s course. That mapping is critical because the treatment approach depends entirely on where the tunnel runs and which muscles it involves.