Gastroenteritis (an intestinal infection or stomach flu) can share many symptoms with Crohn’s disease. Many different factors can cause an intestinal infection, including:

Your doctor will make a diagnosis of Crohn’s disease after they rule out other potential causes of your symptoms. It’s important to understand what an upset stomach involves before assuming you have a more severe medical condition.

The stomach is an organ located in the upper abdomen between the esophagus and the small intestine. The stomach performs the following functions:

  • takes in and breaks down food
  • destroys foreign agents
  • aids in digestion
  • sends signals to the brain when you’re full

The stomach helps prevent infections by secreting an acid from its lining that acts on harmful bacteria and viruses present in food you eat.

The small intestine absorbs most of the nutrients you consume. And the stomach helps break down amino acids and absorbs simple sugars, such as glucose. The stomach also breaks down certain medications, such as aspirin. A sphincter, or valve, at the bottom of the stomach regulates how much food enters the small intestine.

Swelling (inflammation) of the stomach lining and intestines is what characterizes an upset stomach. It is sometimes caused by a virus, although it may also be due to a parasite, or due to bacteria like salmonella or E. coli.

In some cases, an allergic reaction to a certain type of food or an irritation causes an upset stomach. This can happen from consuming too much alcohol or caffeine. Eating too many fatty foods — or too much food — may also cause an upset stomach.

Crohn’s disease is an ongoing (chronic) condition that causes the gastrointestinal (GI) tract to become inflamed. While the stomach may be affected, Crohn’s goes beyond this area of the GI tract. Inflammation may also occur in the:

  • small intestines
  • mouth
  • esophagus
  • colon
  • anus

Crohn’s disease can cause an upset stomach, but you’re also more likely to experience other related symptoms including:

Common symptoms of upset stomach may include:

Fortunately, most cases of upset stomach can be treated without a trip to the doctor. Treatment should focus on replenishing fluids and dietary management. You may also need antibiotics, but only if the stomachache is caused by certain bacteria.

Clear liquids

For adults, the University of Wisconsin-Madison recommends a clear liquid diet for the first 24 to 36 hours of an upset stomach with nausea, vomiting, or diarrhea. Make sure to drink plenty of water, sports drinks, or other clear liquids (2 to 3 liters per day). You should also avoid solid foods, caffeine, and alcohol.

Wait for one to two hours before attempting to drink a small quantity of water if you are also experiencing vomiting. You can suck on ice chips or popsicles. If you tolerate this, you may move on to other clear liquids, including non-caffeinated drinks, such as:

  • ginger ale
  • 7-Up
  • decaffeinated tea
  • clear broth
  • diluted juices (apple juice is best)

Avoid citrus juices like orange juice.


You may attempt to eat bland foods if you tolerate clear liquids. These include:

  • saltine crackers
  • toasted white bread
  • boiled potatoes
  • white rice
  • applesauce
  • bananas
  • yogurt with live culture probiotics
  • cottage cheese
  • lean meat, like skinless chicken

Scientists are exploring the use of probiotics in preventing and treating viral causes of intestinal infections. Studies have indicated that good gut bacteria species like Lactobacillus and Bifidobacteriumhave been shown to decrease the length and severity of diarrhea related to rotavirus infections. Researchers continue to explore the timing, length of use, and amount of probiotics necessary for effective treatment.

The American Academy of Family Physicians says adults may resume a normal diet if symptoms improve after 24 to 48 hours. However, avoid certain foods until your digestive tract has recovered. This may take one to two weeks. These foods include:

  • spicy foods
  • uncultured dairy products (such as milk and cheese)
  • whole grains and other high-fiber foods
  • raw vegetables
  • greasy or fatty foods
  • caffeine and alcohol


Acetaminophen can control symptoms such as fever, headaches, and body aches. Avoid aspirin and ibuprofen because they may cause further stomach irritation.

In adults, an over-the-counter bismuth subsalicylate (such as Pepto-Bismol) or loperamide hydrochloride (such as Imodium) can help control diarrhea and loose stool.

Most symptoms of an upset stomach should subside within 48 hours if you follow the above treatment regimen. If you don’t begin feeling better, Crohn’s disease is only one possible cause of your symptoms.

You should consult a doctor if you have any of the following symptoms along with an upset stomach:

  • abdominal pain that doesn’t improve after either a bowel movement or vomiting
  • diarrhea or vomiting that persists for more than 24 hours
  • diarrhea or vomiting at a rate of more than three times per hour
  • fever of over 101°F (38°C) that doesn’t improve with acetaminophen
  • blood in stool or vomit
  • no urination for six or more hours
  • lightheadedness
  • rapid heartbeat
  • inability to pass gas or complete a bowel movement
  • pus drainage from the anus

Despite the possible causes of an upset stomach, symptoms should eventually go away in a short amount of time and with proper care. The difference with Crohn’s disease is that the symptoms keep coming back or continuing without warning. Weight loss, diarrhea, and abdominal cramps can also occur in Crohn’s. If you experience persistent symptoms, see your doctor. Never self-diagnose chronic symptoms. There is no cure for Crohn’s disease, but you can manage this condition with medications and lifestyle changes.

Talking to others who understand what you’re going through can also make a difference. IBD Healthline is a free app that connects you with others living with Crohn’s through one-on-one messaging and live group chats. Plus, get expert-approved information on managing Crohn’s disease at your fingertips. Download the app for iPhone or Android.



Answers represent the opinions of our medical experts. All content is strictly informational and should not be considered medical advice.
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