A belly button that smells and hurts at the same time almost always points to an infection, either bacterial or fungal. The navel is a small, warm, moist pocket that traps sweat, dead skin, and bacteria, making it one of the most infection-prone spots on your body. Less commonly, a cyst or an anatomical leftover from fetal development can be the source. Here’s how to tell what’s going on and what to do about it.
Bacterial Infection: The Most Likely Cause
The combination of smell plus pain is the hallmark of a bacterial belly button infection. Staph and strep bacteria are the most common culprits, though E. coli and other gut-related bacteria can also be involved. These organisms thrive in the damp folds of the navel, and once they multiply enough, they trigger inflammation.
What you’ll typically notice: redness and swelling around or inside the belly button, tenderness when you touch it, and a discharge that may look cloudy, yellowish, or greenish. The discharge is what produces the foul smell. Some people describe it as a sharp, sour, or “cheese-like” odor. The skin surrounding the navel may feel warm and look puffy or discolored.
Minor bacterial infections sometimes start after you’ve been picking at your belly button, after a piercing, or simply from not drying the area well after a shower. Moisture left sitting in a deep navel creates the perfect environment for bacteria to take hold.
Yeast and Fungal Infections
Yeast (most often Candida) can overgrow inside the belly button, especially if the area stays warm and damp for long stretches. This is more common in people with deeper navels, higher body weight, or those who sweat heavily. A yeast infection typically looks like a bright red rash in the skin folds of the navel, and it’s usually intensely itchy. It may burn. You might also notice scaling, swelling, or a white discharge.
Yeast infections on their own don’t always produce a strong odor. But if the yeast infection develops alongside a skin condition called intertrigo (where skin folds rub together and trap moisture), you may notice a musty smell. Pain from a yeast infection tends to feel more like burning or raw irritation rather than the deep tenderness of a bacterial infection.
Cysts That Rupture or Get Infected
Epidermal inclusion cysts (sometimes called sebaceous cysts) can form in or near the belly button. These develop when skin cells get pushed beneath the surface, often after minor trauma, and create a small pocket that fills with a protein called keratin. You might not even know you have one until it gets infected or ruptures.
When one of these cysts breaks open, it releases thick, yellow fluid that has a distinctly foul odor. The area becomes swollen, painful, and discolored. If you’ve noticed a small, firm bump near your belly button that suddenly became painful and started leaking smelly fluid, a ruptured cyst is a strong possibility. These need to be drained properly to prevent the infection from worsening or recurring.
Urachal Remnants: A Hidden Cause
Before you were born, a small tube called the urachus connected your umbilical cord to your bladder. It normally closes up and disappears before birth, but in some people, a small remnant persists. This leftover tissue can form a fluid-filled pocket called a urachal cyst, which sits deep behind the belly button.
Most people with a urachal remnant never know it’s there. Problems show up only if the cyst becomes infected, which can cause abdominal pain centered around the navel, fever, pain during urination, and sometimes drainage from the belly button itself. This is less common than a simple skin infection, but it’s worth knowing about because it won’t resolve with surface-level cleaning or topical treatments alone.
How to Tell It Apart From a Hernia
An umbilical hernia can also cause belly button pain, and people sometimes confuse hernias with infections. The key difference is what you see and feel. A hernia produces a soft bulge near the navel that gets bigger when you cough, strain, or bear down. You can often push it back in. There’s no discharge and no smell.
An infection, by contrast, produces redness, swelling that doesn’t reduce with pressure, and typically some kind of discharge or crusting. If you have a bulge that becomes firm, painful, and discolored and you can no longer push it back in, that’s a hernia that may have become trapped (incarcerated), which needs urgent medical attention for different reasons than infection.
Warning Signs That Need Immediate Attention
Most belly button infections are mild and stay local. But a navel infection can, in rare cases, progress quickly into something serious. Omphalitis (the medical term for an infected umbilical area) is classified as a medical emergency when it spreads, because the tissue in and around the navel connects to deeper structures in the abdominal wall.
Watch for these red flags: redness that’s spreading outward from the belly button across your abdomen, fever, feeling unusually tired or unwell, or skin that looks dark, blistered, or crackly around the navel. Rapidly spreading redness combined with high fever and feeling systemically sick could indicate the infection has entered the bloodstream or is damaging deeper tissue. If the area is getting visibly worse over hours rather than days, get medical care right away.
How to Clean and Care for Your Belly Button
For a mild case with just a bit of odor and minor soreness, proper cleaning is the first step. Soap and water is all you need. A dermatologist-recommended approach: lather a mild, fragrance-free soap onto a cotton swab or the corner of a washcloth, then gently work it around the inside of your belly button to remove dirt and debris. Don’t scrub aggressively. Tiny tears in the delicate skin inside the navel can actually introduce more bacteria and make things worse.
After cleaning, dry the inside of your belly button thoroughly with a clean cotton swab or dry towel corner. This step matters more than most people realize, because lingering moisture is exactly what feeds bacterial and fungal growth. Avoid putting lotion or moisturizer inside your navel. It’s already a naturally moist environment, and adding moisture only encourages more bacterial overgrowth.
If gentle daily cleaning for a few days doesn’t resolve the smell and pain, or if you notice increasing redness, worsening discharge, or any of the red flags above, the infection likely needs medical treatment. Bacterial infections typically require a course of antibiotics (topical or oral depending on severity), while fungal infections are treated with antifungal creams. Cysts and urachal remnants usually need to be addressed with a procedure to drain or remove the underlying structure.