Why Do I Have 2 Holes in My Bum? Causes Explained

Finding what looks like a second opening near your anus is almost always explained by one of a handful of well-understood conditions, not by an anatomical abnormality you were born with. The most common culprits are a pilonidal sinus, an anal fistula, or a congenital dimple that was always there but only recently caught your attention. Each has different causes, sits in a slightly different spot, and calls for a different response, so figuring out which one you’re dealing with matters more than you might think.

Pilonidal Sinus

A pilonidal sinus is probably the single most common reason someone notices a second “hole” in the area between the buttocks. It typically appears as a small pit or opening in the natal cleft, the crease that runs between your buttock cheeks, usually a few centimeters above the anus and closer to the tailbone. When it becomes infected, it can swell into a painful, reddened lump that drains pus or blood, and that draining opening is often what people first notice as an unexplained second hole.

The condition develops when loose hairs burrow into the skin of the natal cleft. Friction, sweating, and pressure push hairs beneath the surface, where the body treats them as foreign material and walls them off in a small cavity lined with skin cells. Over time that cavity can become a chronic sinus tract with one or more visible openings on the surface. The sepsis from a pilonidal sinus tends to stay in the tissues overlying the coccyx and sacrum and does not communicate with the inside of the anal canal, which is a key feature that distinguishes it from an anal fistula on imaging.¹

Pilonidal sinuses are far more common in young men, particularly those with coarse or abundant body hair, though anyone can develop one. Sitting for long periods is a well-known risk factor, and the condition was once nicknamed “Jeep Disease” because it was so prevalent among military drivers during the Second World War.² If you work a desk job or drive for a living, the combination of pressure and warmth in that crease creates an environment where hairs are more likely to become trapped.

Anal Fistula

An anal fistula is a small tunnel that forms between the inside of the anal canal and the skin near the anus. Its external opening looks like a tiny hole, sometimes leaking fluid or pus, and sits closer to the anus than a pilonidal sinus does. Because the tunnel actually connects to the anal canal internally, the discharge sometimes includes mucus or has a fecal odor, which is something you would not see with a pilonidal sinus.

Most fistulas start life as a perianal abscess. Tiny glands inside the anal canal can become blocked and infected, and when the resulting abscess drains or is drained surgically, it sometimes leaves behind a persistent tunnel. Roughly four in ten perianal abscesses go on to produce a fistula.³ The initial infection usually involves gut bacteria, though once the fistula becomes chronic, bacteria are less consistently found within the tract itself.⁴

Fistulas can be straightforward or complex, with some tracts branching or looping around the sphincter muscles. MRI is considered the best imaging tool for mapping them before any surgical decision is made, because it shows both the extent of the tract and its relationship to the muscles that control continence.⁵ Getting that roadmap right is critical: a surgeon who cuts through sphincter muscle without knowing the full anatomy risks damaging continence.

How to Tell the Two Apart

Location is the simplest clue. A pilonidal sinus sits higher up, in the midline crease between the buttocks, often at or above the level of the tailbone. An anal fistula opens closer to the anal margin, sometimes right beside it. The character of the discharge also differs: a pilonidal sinus tends to drain thicker pus, sometimes with hair visible in it, while a fistula may produce thinner, more watery or mucoid discharge.

In ambiguous cases, MRI can reliably distinguish the two. In one study comparing the conditions, the hallmark of an anal fistula was a connection through the sphincter muscles to the inside of the anal canal, while a pilonidal sinus lacked any such communication and instead tracked through the superficial tissues over the tailbone.¹ Your doctor can usually tell by physical exam alone, but imaging becomes important when surgery is on the table.

Congenital Sacrococcygeal Dimples

Sometimes what you’re noticing is not new at all. Sacrococcygeal dimples are small indentations in the skin near the base of the spine that are present from birth. Many people go their whole lives without realizing they have one, only to discover it while showering or during a partner’s observation and assume something is wrong. Most of these dimples are completely harmless.

Researchers have classified these dimples by their position relative to the gluteal crease. A dimple sitting within the crease itself, including the small “coccygeal pit” that many people have, carries a low risk of being associated with any underlying spinal issue. In one study, only about one in six infants with this type of dimple had any underlying spinal abnormality. But dimples located at the upper edge of the crease or above it were associated with spinal findings like lipomas or tethered filaments in roughly half of cases.⁶ So a shallow dimple sitting low and centered in the crease is almost certainly nothing to worry about, while a dimple that sits noticeably above the crease line or is accompanied by a skin tag, tuft of hair, or discoloration may be worth having checked.

Anal Canal Duplication

This is the rarest explanation by far, but it’s worth mentioning because it is literally a second anal opening. Anal canal duplication is a congenital anomaly in which a second channel is present near the anus. Despite looking like a second anus, it typically does not connect to the rectum and has no functional role in passing stool.⁷

Because it is so uncommon, anal canal duplication is often misdiagnosed at first as a hemorrhoid, an abscess, or a fistula. It usually sits behind the normal anus and may produce no symptoms at all. However, surgeons generally recommend removing it when it is identified, because of the risk of infection over time and, in very rare cases, the risk of cancerous changes within the lining of the duplicate canal.⁸

When an Underlying Disease Is the Driver

In some people, a second opening near the anus is not a standalone problem but a symptom of a broader inflammatory or skin condition. Two diseases are especially worth knowing about.

Crohn’s disease, a chronic inflammatory bowel condition, is one of the better-known causes of complex anal fistulas. Perianal fistulas are a frequent complication and can be the first sign that Crohn’s is present, sometimes appearing before any gut symptoms. These fistulas tend to be harder to treat than garden-variety ones, and the standard approach involves a combination of surgery and medication. Even with that combined strategy, long-term remission is achieved in only about half of Crohn’s-related perianal fistula cases at best.⁹ If you’re developing recurrent abscesses or fistulas, especially alongside changes in bowel habits, weight loss, or abdominal pain, it’s worth asking your doctor about screening for inflammatory bowel disease.

Hidradenitis suppurativa is a chronic skin condition that causes painful lumps and draining tracts in areas where skin rubs together. When it affects the gluteal fold, it can look almost identical to a pilonidal sinus. In a large study of over 2,400 patients with hidradenitis suppurativa, about a quarter reported lesions in the intergluteal fold. Among those whose clinical diagnosis was confirmed, roughly one in five actually had hidradenitis suppurativa in that location rather than a true pilonidal sinus, while the rest did have pilonidal disease.¹⁰ Patients with more severe hidradenitis and those who smoked were more likely to have intergluteal involvement. This overlap matters because hidradenitis requires different long-term management than a simple pilonidal cyst; misdiagnosis can lead to repeated failed surgeries.

What an Infected Pilonidal Sinus Actually Looks Like Under the Microscope

When a pilonidal sinus gets infected, the bacterial community inside it is surprisingly diverse. A study of pus aspirated from 75 infected sinuses found bacterial growth in every single case, with anaerobic organisms (the kind that thrive without oxygen) dominating. About three-quarters of the specimens grew only anaerobes, while mixed aerobic and anaerobic populations showed up in roughly one in five.¹¹ The mix of gut-related bacteria like Bacteroides and E. coli reflects the location: trapped in a warm, moist crevice right next to the bowel, these sinuses essentially create a mini-ecosystem that the body cannot clear on its own once the cavity has formed. That’s why antibiotics alone rarely cure a pilonidal sinus; the cavity itself needs to be addressed.

Treatment Depends on Which Condition You Have

For pilonidal sinuses, treatment ranges widely depending on severity. A first-time acute abscess can sometimes be drained in a clinic with a local anesthetic. Chronic or recurrent disease generally requires surgery. The field has moved toward less invasive techniques: a procedure called pit-picking, which removes only the sinus pits and a minimal amount of tissue, resulted in significantly less pain and faster healing than traditional radical excision in a randomized trial. Patients who had pit-picking reached complete wound healing in a median of about 17 days compared to 60 days for the wider excision, and the failure rates were similar between the two approaches.¹²

Laser techniques are also gaining ground. A comparative review found that laser-assisted procedures shortened hospital stays dramatically (often just a few hours versus days), reduced pain, and achieved healing rates as high as 97 percent. The trade-off is cost: laser equipment and expertise make the procedure more expensive, and for severe or complicated sinuses, traditional surgery may still be necessary.¹³

For anal fistulas, the approach depends on how the tract relates to the sphincter muscles. Simple fistulas that pass through little muscle tissue can be laid open in a single procedure. Complex fistulas that wind through the sphincter need staged treatment, sometimes involving a flexible thread called a seton that is threaded through the tract and left in place for weeks or months to promote gradual drainage and healing without damaging the muscle. Newer options include plugs, fibrin glue, and a technique that lifts the internal opening of the fistula away from the sphincter.

Preventing Recurrence

Pilonidal disease is notorious for coming back. One of the most effective adjuncts to surgery is laser hair removal in the natal cleft. Removing the hair that originally caused the problem reduces the likelihood that new sinuses will form. In one early series, recurrences occurred almost exclusively in patients who did not maintain hair removal and hygiene afterward.¹⁴ A separate study came to the same conclusion, recommending that laser depilation combined with patient education on hygiene should be offered routinely to all pilonidal sinus patients after surgery.¹⁵

Beyond laser removal, practical steps include keeping the area clean and dry, avoiding prolonged sitting on hard surfaces when possible, and wearing loose-fitting underwear to reduce friction. None of these measures are guaranteed to prevent a first episode, but they meaningfully reduce the odds of a recurrence after treatment.

When to Get It Checked Urgently

Most pilonidal sinuses and fistulas are uncomfortable but not dangerous. The exception is when infection spreads beyond the local area. Complicated perianal sepsis, though uncommon, can progress to necrotizing fasciitis or spread into the abdominal cavity. A case series documented patients who presented with these rare but serious sequelae, all of whom required aggressive surgical intervention.¹⁶ If you notice rapidly spreading redness, fever, severe pain out of proportion to the size of the lump, or if you feel generally unwell, those are reasons to seek medical attention the same day rather than waiting for a scheduled appointment.

Even outside an emergency, any persistent opening that drains fluid deserves evaluation. A fistula that is left to smolder indefinitely can become more complex over time, making eventual surgery harder. And as noted, recurrent or multiple openings can sometimes be the first visible clue to Crohn’s disease or hidradenitis suppurativa, conditions where early diagnosis changes the treatment trajectory significantly.

The Quality-of-Life Side That Nobody Talks About

One of the less discussed aspects of having a draining sinus or fistula near the anus is how much it affects daily life. Embarrassment, anxiety about odor, and the logistics of wound care can be genuinely isolating. In interviews with pilonidal sinus patients, recurring themes included embarrassment, a feeling of lost control over their own body, and changes in body image.¹⁷

The burden is especially significant for adolescents, who make up a large proportion of pilonidal patients. In a survey of teenagers awaiting treatment, about two-thirds reported that daily activities were moderately or severely affected, and well over half said their ability to play sports was impacted. Nearly half reported interference with school or work attendance.¹⁸ These numbers were collected before treatment; most patients reported substantial improvement afterward. The takeaway is that seeking treatment is not just about avoiding a rare complication. It’s about reclaiming a normal routine, and there’s no reason to tolerate months of discomfort out of embarrassment when effective options exist.