A fissure is a tear in the lining of the anal canal, while a fistula is an abnormal tunnel that forms between the inside of the anal canal and the skin near the anus. They share a location and some overlapping symptoms, but they have different causes, feel different, and require different treatments. Understanding which one you’re dealing with matters because a fissure often heals on its own, while a fistula almost always needs surgery.
What Each One Actually Is
An anal fissure is a small crack or split in the thin tissue lining the anus, similar to a paper cut. It sits on the surface and doesn’t extend deeper into surrounding tissue. Most fissures occur along the back wall of the anal canal, where blood flow is poorest and the tissue is most vulnerable to tearing.
An anal fistula is a tunnel-like tract that connects two surfaces that shouldn’t be connected, typically the inside of the anal canal to the skin surrounding the anus. This tunnel becomes lined with tissue over time, which prevents it from closing on its own. Fistulas can be straightforward, running in a simple path just beneath the skin, or complex, branching through the muscles that control bowel movements. The complexity of the tract determines how difficult it is to treat.
How They Develop
Fissures are mechanical injuries. The most common cause is passing hard, dry stool that stretches and tears the anal lining. Chronic constipation and straining are the biggest risk factors, but chronic diarrhea, childbirth, and penetration can also cause them. Conditions like inflammatory bowel disease or prior anal surgery make the tissue more vulnerable to tearing.
Fistulas develop through a completely different process. Most begin with an infection in one of the small glands inside the anal canal. These glands sit in the space between the two rings of muscle that form the anal sphincter. When a gland becomes blocked, bacteria build up and create an abscess, essentially a pocket of pus. Once that abscess drains (either on its own or with medical help), the path it carved through the tissue can persist as a permanent tunnel. This is the cryptoglandular theory first described by Parks in 1961, and it explains the majority of cases.
Crohn’s disease is the other major cause of fistulas. Up to 50% of people with Crohn’s develop a fistula within 20 years of their initial diagnosis, and roughly 75% of those fistulas are classified as complex, meaning they involve significant portions of the sphincter muscle or have multiple branching tracts.
How the Symptoms Differ
The pain patterns are the clearest way to distinguish between the two. A fissure causes sharp, cutting pain during a bowel movement, often described as passing broken glass. This pain can linger for minutes to hours afterward. You’ll typically see bright red blood on the toilet paper or on the surface of the stool. There may be itching or irritation, and if you look, you can sometimes see a visible crack in the skin around the anus.
A fistula produces a different set of symptoms. The hallmark is persistent drainage of pus or blood from a small opening near the anus. This drainage often stains underwear and may have an unpleasant odor. You might notice swelling or a tender lump near the anus that comes and goes as the tract fills and drains. Pain tends to be more constant rather than tied specifically to bowel movements, and if the tract becomes blocked and re-infected, fever and chills can develop.
How Each Is Diagnosed
Fissures are usually diagnosed with a simple visual examination. A doctor can often see the tear by gently separating the skin around the anus. No imaging or special tools are typically needed, though chronic fissures sometimes develop a small skin tag at the outer edge that can be a clue.
Fistulas require more investigation. The external opening may be visible as a small, draining hole near the anus, but the real question is where the internal opening sits and what path the tunnel takes through the surrounding muscle. MRI and endoanal ultrasound are the two standard imaging tools used to map fistula tracts before any surgical plan is made. Getting this map right is critical because the surgical approach depends entirely on how much sphincter muscle the tract passes through.
Treatment for Fissures
Most acute fissures heal within a few weeks with conservative care. The goal is to soften stool and reduce pressure on the anal canal. Drinking more water, eating more fruits and vegetables, and using a stool softener all help. A small step stool under your feet while sitting on the toilet positions your hips in more of a squatting angle, which reduces straining. Warm sitz baths, where you soak the area in a few inches of warm water for 15 to 20 minutes, three to four times a day, can relieve pain and improve blood flow to the area.
Fissures that don’t heal after several weeks of home care are considered chronic. At that point, a prescription ointment that relaxes the internal sphincter muscle can help. These ointments work by increasing blood flow to the tear, which promotes healing. A typical course is applied twice daily for up to three to six weeks.
If topical treatment fails, a minor surgical procedure called a lateral internal sphincterotomy is the next step. This involves making a small cut in the internal sphincter muscle to reduce the spasm that prevents healing. It has a 96% healing rate, with most fissures closing within about three weeks of the procedure.
Treatment for Fistulas
Fistulas do not heal with ointments, sitz baths, or dietary changes. The tissue lining the tunnel prevents it from closing, so surgery is the standard treatment. The specific approach depends on how much sphincter muscle is involved.
Simple fistulas that pass through little or no sphincter muscle can be treated with a fistulotomy, where the surgeon opens the entire tract, converting the tunnel into an open groove that heals from the bottom up. This is the most straightforward option and has high success rates.
Complex fistulas that pass through a significant portion of the sphincter require a more careful approach because cutting through too much muscle risks affecting bowel control. In these cases, a seton (a thin loop of material threaded through the fistula tract) is often placed. The seton keeps the tract open and draining, prevents new abscesses from forming, and can gradually help the tissue heal over weeks to months. Some complex fistulas require staged procedures or more advanced surgical techniques to close the internal opening while preserving muscle function.
Recovery from fistula surgery is generally longer and more involved than fissure surgery. The wound is left open to heal from the inside out, which means daily wound care, sitz baths, and follow-up visits to make sure the tract is closing properly. Simple fistulotomies may heal in four to six weeks, while complex fistulas treated with setons can take several months.
Can One Lead to the Other?
A fissure does not turn into a fistula. They develop through entirely different mechanisms: one is a surface tear caused by mechanical trauma, the other is a deep tunnel caused by infection. However, both conditions can coexist, and both are more common in people with Crohn’s disease or other inflammatory bowel conditions. A perianal abscess is the bridge between a healthy anal canal and a fistula. If you’ve had an abscess drained near the anus, there’s a meaningful chance a fistula will develop in the weeks or months that follow, so it’s worth paying attention to any ongoing drainage from the area.