Waking Up to Poop? Here's What Your Body's Trying to Tell You

Getting up in the middle of the night to use the bathroom can be disruptive — and possibly a sign of a bigger issue.
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You might wake up in the middle of the night to pee on occasion, but rising at 3 a.m. with the urge to poop? Now, that's a different story.


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It also should make you sit up and ask yourself: What could be going on?

"Nocturnal bowel movements are considered an 'alarm symptom' and can signal something is wrong," says Maia Kayal, MD, assistant professor in the division of gastroenterology at the Icahn School of Medicine at Mount Sinai, tells LIVESTRONG.com.

There may be some factor that over-activates bowel receptors to stimulate an overnight BM or causes damage to the bowel wall, Dr. Kayal explains.


Here's what might be going on if you're waking up with the urge to go:

1. You Have an Infection

A gastrointestinal infection can be caused by bacteria or viruses. If you get the stomach flu, for instance, watery diarrhea might be accompanied by abdominal cramping, nausea and vomiting, or a low-grade fever, according to the Mayo Clinic.


It can be hard to hear, but you're probably going to have to ride this out.

"In most cases, vital GI infections ease up on their own. Patients just have to take it easy and replenish their fluids consistently," Niket Sonpal, MD, a New York City-based internist and gastroenterologists, says.

If you do see a doctor, they might opt to take a stool sample to identify the bacteria or virus at play and recommend treatment from there, Dr. Sonpal says.


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2. You Have a Digestive Condition

Inflammatory bowel disease (IBD) includes Crohn's disease and ulcerative colitis; they are marked by long-term inflammation that eventually damages the GI tract, according to the CDC. IBD flares can affect you at night, waking you up to poop, Dr. Kayal says.

What differentiates IBD from another cause are other symptoms that tag along with night poops.


"Patients will typically have other symptoms such as weight loss, abdominal pain, bloody diarrhea, fecal urgency or oral ulcers in addition to nocturnal bowel movements," Dr. Kayal says.

You'll want to pay attention to how long you've been dealing with this nighttime disturbance.

Waking up to poop every once in a while might not actually be a problem, Dr. Sonpal says, but "if it becomes a chronic, regular occurrence where you are sleeping and being woken up and physically compelled to go relieve yourself, that could signal something that needs a doctor's attention."


You'll need to schedule an in-person — not virtual visit — Dr. Sonpal says. Endoscopy, colonoscopy, MRI or CT scans, as well as stool samples and blood tests may all be used in diagnosis, the CDC notes.

It's also worth noting that irritable bowel syndrome (IBS) is not typically associated with middle-of-the-night BMs, Dr. Kayal says.

3. You Have Food Poisoning

The chicken you ordered didn't look suspect or the tuna poke bowl tasted just fine, but here you are, spending your night running to the bathroom.


Foodborne "GI infections cause activation of the immune system and the release of inflammatory mediators and cytokines that can directly act on the bowel and stimulate diarrhea," Dr. Kayal says.

They can also produce toxins that damage the bowel, another factor that contributes to loose stools, she says.

It might be agony now, but you'll slowly recover.


In the meantime, diarrhea — especially a bad case — can cause dehydration if you're not consuming liquids like water and soup.

See your doctor if you also have a fever, bloody diarrhea, severe abdominal pain or have dark urine or get dizzy with standing, two symptoms of dehydration, Dr. Kayal says.

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4. Your Medication Has Some Surprising Side Effects

Are you taking a new medication?

If the middle-of-the-night urge is new, consider any recently prescribed or OTC medication that you're taking. Dr. Kayal adds that medications like antibiotics, NSAIDs (like ibuprofen), chemotherapy drugs and drugs that contain magnesium (like antacids) may all be culprits.

Antibiotics, for example, can change the balance of gut bacteria, leading to diarrhea. Before taking an anti-diarrheal medication to stop the runs, talk to your doctor.

5. It’s Something Else

Hyperthyroidism (an "overactive thyroid") and neuroendocrine tumors are two additional conditions to have on your radar if you're experiencing nighttime BMs, Dr. Kayal says.

Neuroendocrine tumors (NETs) are cancerous tumors that can occur anywhere on the body, including in the GI system like the small intestine, rectum and pancreas, per the Mayo Clinic.

"These conditions cause increased bowel movements in general by acting on different bowel receptors or by damaging the bowel lining," Dr. Kayal says.

In addition to diarrhea, you might also experience unintentional weight loss and fatigue. Talk to your doctor who can conduct tests to rule out IBD or other diseases that affect your digestive system.

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Is this an emergency? If you are experiencing serious medical symptoms, please see the National Library of Medicine’s list of signs you need emergency medical attention or call 911.