Causes of Severe Stomach Pain & Diarrhea in The Middle of the Night.

Our content is not intended nor recommended as a substitute for medical advice by your doctor. Use for informational purposes only.

What you need to know:

The cause of severe stomach pain and diarrhea depends on the time frame of your symptom.

The recent onset of severe abdominal pain and diarrhea in the middle of the night is often due to infections and foodborne illnesses (food poisoning). Chronic or recurrent night diarrhea and stomach pain incursions have a wider range of possible causes. 

Today, You will learn about the distinguishing features of each cause. Although a gastroenterologist writes the article, please don’t use it as a substitute for medical advice.

Causes of acute attack:

  • Infection (gastroenteritis).
  • Food poisoning (foodborne illness).
  • An acute attack of food intolerance or allergy.
  • Recent intake of a drug that causes diarrhea.

Causes of chronic attacks:

  • Food intolerance.
  • Celiac disease.
  • IBD.
  • Chronic infections
  • Bile acid diarrhea.
  • Drug-induced diarrhea
  • Less frequent causes: Endocrinal disease, SIBO, chronic pancreatitis, diabetes, and others.  

Below, we will explain the symptoms & features of the common causes.

1. Acute gastroenteritis.

Gastroenteritis is the infection of your stomach, intestine, and colon with bacteria, viruses, or other organisms such as protozoa.

The sudden onset of severe stomach pain and diarrhea in the middle of the night usually indicates an attack of acute gastroenteritis (or food poisoning).

Cause and transmission:

The most common cause of acute gastroenteritis is viruses (reference). The common infectious organisms are summarized below:

  • Viruses (0norovirus, rotavirus, adenovirus, astrovirus, and others).
  • Bacteria (salmonella, campylobacter, shigella, E. coli, and others.
  • Protozoa (Giardiasis, Cryptosporidium, cyclosporine, Entamoeba, and others).

Transmission is usually acquired by eating or touching infected food or surfaces (fecal-oral route).


Bacterial diarrhea is usually a more severe form. High-grade fever, extreme abdominal pain, and bloody diarrhea often indicate a bacterial cause

Viral gastroenteritis is known as stomach flu (the most common cause). Stomach flu has a milder nature. Fever may be absent or of low grade with stomach flu.

Symptoms of viral gastroenteritis:

  • Sudden onset diarrhea (watery, usually yellowish or light brown).
  • Sudden onset abdominal pain (usually in colics, affects your whole abdomen. However, it is more prominent in the lower abdomen.
  • Diarrhea and severe stomach pain start any time of the day, including in the middle of the night. 
  • Nausea and maybe vomiting.
  • Low-grade fever.
  • Muscle aches.
  • Anorexia. 
  • Headache.

The differences between viral and bacterial gastroenteritis are enlisted in the below table.

TypeViral GastroenteritisBacterial gastroenteritis
1- SiteUsually affects the stomach and small intestine.Affects the colon.
2- Diarrhea.Watery, mildbloody, mucoid, more severe.
3-Vomitingusually presentrarely occur.
4- Crampsmildsevere
5- Feverlow gradehigh grade
6- Anorexiamild or not presentsevere.

2 . Foodborne illnesses (food poisoning):

Food poisoning is an illness caused by bacteria or other toxins in food. It typically causes diarrhea, vomiting, and abdominal pain. But it can lead to non-gastrointestinal symptoms, which can be severe.


  • Food contamination with bacteria, viruses, or toxins.
  • Bacteria: Campylobacter, clostridium botulinum, Clostridium perfringens, E. coli, salmonella, shigella, staph. aureus, and others.
  • Viruses: Hepatitis A virus, Rotavirus, Norovirus.
  • Protozoa as giardia lamblia.

Symptoms of food poisoning:

  • The symptoms start suddenly, often more severe than viral gastroenteritis (especially in bacterial organisms).
  • Vomiting: it can be mild or severe. 
  • Severe stomach pain.
  • Diarrhea; can be severe (high frequency). Sometimes, you pass only mucus or bloody stool.
  • Fever, which can be high grade.
  • Complications: severe dehydration and electrolyte disturbance, and shock affect risk groups (elderly, infants, pregnant women, and people with chronic diseases).

Learn More about food poisoning.

3 . Food intolerance or allergy.

You may wake up in the middle of the night with a sudden attack of abdominal pain and diarrhea. The answer to the cause may be in the food you ate before this attack.

Your digestive system may have trouble digesting and absorbing specific types of food. The undigested/unabsorbed food inside your intestine may cause intolerance symptoms (such as diarrhea and abdominal pain). 

The above condition is known as (food intolerance). Food intolerance is different from food allergy. Food allergy is an immune-mediated reaction to certain types of food. 

Common causes of food intolerance and allergy include:

  • Lactose intolerance (dairy products).
  • Fructose malabsorption.
  • Alcohol intolerance.
  • FODMAP intolerance (as with People with IBS).
  • Amines, salicylate, sulfite intolerances.
  • Caffeine intolerance.
  • Raw meat, seafood.
  • Nuts, peanut
  • Mustard.
  • Rice
  • Some vegetables and fruits.

The differences are enlisted in the below table.

Food intoleranceFood allergy
Affects 15-20% of the populationAffects nearly 2-5% of adults
Difficulty digesting certain types of food (not immune-mediated allergy). An immune-mediated reaction to certain foods or food components.
Causes “recurrent acute” or “chronic” attacks of diarrhea (which can be bright yellow & watery).Usually causes acute attacks related to the ingestion of offending food.
Intestinal symptoms: diarrhea, extensive gas, bloating, and abdominal painIntestinal symptoms are the same
No extraintestinal symptomsExtraintestinal symptoms like rashes, urticaria, swollen lips or face, or severe life-threatening allergic reactions.
The severity of your symptoms is proportional to the amount you eat from the offending food.Even trace amounts of the offending food can produce severe symptoms.

Common offending foods: 

  • Lactose intolerance (dairy products).
  • Fructose malabsorption.
  • alocholintolerance.
  • FODMAP intolerance (as with People with IBS).

Common offending foods: (examples) 

  • Raw meat, seafood.
  • Nuts, peanut
  • Mustard.
  • Rice
  • Some vegetables and fruits.

4. Celiac disease:

Celiac disease is an extreme form of food allergy. An immune reaction to eating gluten (in wheat, rye, and barley) leads to severe diarrhea and stomach pain.

People who stop eating gluten improve dramatically. No other cures are available for it.

Symptoms of celiac disease:

  • Diarrhea: each time you eat gluten.
  • Stomach pain (can be severe and awaken you in the middle of the night).
  • Flatulence and bloating.
  • Nausea and vomiting.
  • Sometimes, it presents with constipation.
  • Malabsorption of nutrients leads to anemia (fatigue, shortness of breath, rapid heartbeats) and weak bones.
  • Itchy, blistery skin rash (dermatitis).
  • Headache.
  • Numbness, tingling in the feet and hands.
  • Joint pain.

The symptoms are either chronic or come in attacks over a long period.

Learn more about celiac disease.

5 . Inflammatory bowel disease.

Inflammatory bowel disease affects about 0.9% (1.8 million) of US adults. It refers to two conditions:

  • Crohn’s disease: Unexplained inflammation and ulceration at any part of your gut (from the mouth to the anus).
  • Ulcerative colitis: Unexplained inflammation and ulceration affecting your large intestine only (the colon and the rectum).


  • Persistent or recurrent diarrhea.
  • Stomach pain. 
  • Diarrhea and stomach pain can be severe enough to awaken you at midnight. 
  • Blood or blood and mucus coming out with or without a stool.
  • Weight loss.
  • Generalized fatigue.
  • Fever may occur.
  • Loss of appetite.

Learn more about IBD.

6. Chronic infections of your gastrointestinal tract. 

Some infectious agents tend to settle inside your gut and cause chronic symptoms. 

Night diarrhea and abdominal pain can be a sign of chronic infection. 

Common causes (organisms) include:

  • Closteroides difficile.
  • Aeromonas.
  • Giardia.
  • Amebae.
  • Campylobacter.
  • Cryptosporidium.
  • Cyclospora.
  • Whipple’s disease.

Diarrhea can be watery, with or without blood and mucus. You may also experience fever, symptoms of malabsorption, and weight loss.

Often, chronic infections affect people with a weak immune system, as with chronic diseases and immunosuppressive drugs).

Learn more.

7 . Bile acid diarrhea.

The inability of your intestine to handle bile can result in a severe form of diarrhea called bile acid diarrhea. 

Excess bile acid secretion or malabsorption of the bile acid leads to Bile acid diarrhea.

The following facts and statistics will help you imagine the amplitude of BAD:

  • About 25 to 50% of patients diagnosed with IBS-diarrhea have BAD (reference).
  • About 1% of the population may have BAD.
  • About 64% of patients with Functional diarrhea have BAD (reference).
  • Up to 35% of people with a condition called (microscopic colitis) have BAD (reference).

Symptoms suggest Bile acid diarrhea.


  • Diarrhea: especially after fatty meals. It can awaken you at night.
  • Extreme urgency: a sudden severe urge to poop.
  • Extreme urgency may lead to soiling accidents (stool incontinence) in some people.
  • Stomach pain. 
  • Unlike IBS, diarrhea can occur at night (it awakens you from sleep).
  • Stomach gurgling after meals.
  • Bloating and flatulence.

MORE: Constant Diarrhea & Abdominal Pain: 8 Causes Simplified. 

8 . Others.

The below causes are either less frequent or less likely to awaken you at night (as IBS)

  • Irritable bowel syndrome (IBS): although IBS is a common cause of diarrhea and stomach pain, it seldom leads to night diarrhea.
  • Endocrinal diseases such as hyperthyroidism.
  • Small bowel bacterial overgrowth]
  • lymphoma
  • chronic pancreatitis
  • Diabetes.
  • cystic fibrosis