What is Malabsorption Syndrome?

Medically Reviewed by Minesh Khatri, MD on March 25, 2023
4 min read

When you eat a healthy meal, you expect your body to reap the benefits of the vitamins and minerals. But a condition called malabsorption syndrome means your body isn’t able to take in many of the nutrients from the food you eat.

This digestive problem can lead to symptoms such as bloating and diarrhea.

More importantly, malabsorption syndrome can cause serious complications, including a higher chance of infection and bone fractures.

Normally, you absorb most of your nutrients into your bloodstream through the wall of your small intestine as partially digested food works its way through your digestive system. (You absorb the rest of your nutrients through the large intestine.)

Your blood then carries nutrients, such as calcium or protein, to your bones, muscles, and organs. You expel what’s left over through your rectum when you go to the bathroom.

Several medical conditions can interfere with that process.

Infections from bacteria, viruses, or parasites can damage your intestinal wall so that digested substances can’t get through. You then lose those nutrients through your stool when you go to the bathroom.

Some of the other causes of malabsorption include:

  • Cystic fibrosis, chronic pancreatitis, and other diseases that affect the pancreas
  • Lactose intolerance or other enzyme-related conditions
  • Intestinal disorders such as celiac disease (when the gluten protein from wheat, barley, and rye triggers your immune system to attack your body)
  • Severe congestive heart failure which causes the bowel wall to become swollen with fluid (edema) and doesn't absorb nutrients well.

Some of these causes make more sense when you consider how they affect your digestive system.

For example, surgery that removes part of the small intestine means you have less surface area in your remaining small intestine to absorb nutrients.

And celiac disease may injure the walls of your intestinal tract, making it harder for nutrients to be absorbed into the bloodstream.

Malabsorption causes abdominal discomfort, including gas and bloating. Other symptoms you may have:

  • Frequent diarrhea
  • Bad-smelling and loose stool
  • Stools that are light in color or bulky
  • Stools that are hard to flush away because they float or stick to the toilet bowl
  • Weight loss
  • Scaly skin rashes

Chronic (or ongoing) diarrhea is a very common sign of malabsorption. See your doctor if you have symptoms.

If your body isn’t getting the vitamins, minerals, and other nutrients it needs to stay strong and thrive, you could have serious complications. When it’s not treated, malabsorption syndrome might lead to:

  • Greater chance of infections
  • Osteoporosis (low bone density), which increases risk of bone fractures
  • Slower growth and weight gain in children

Certain nutrients, such as vitamin A and zinc, are vital for a healthy immune system and proper growth. If your body isn’t absorbing these and other important vitamins and minerals, your health can suffer.

Children with a bad stomach flu may have a greater chance of a short-term bout of malabsorption syndrome.

You may not need treatment for a short-term problem. Ongoing malabsorption syndrome is more likely if you have one of the following digestive diseases:

Other things that can increase your chances of having the syndrome:

  • Using laxatives or taking antibiotics for a long time.
  • Intestinal surgery
  • Traveling to places known for intestinal parasites


When your doctor suspects malabsorption syndrome, they will need to know your symptoms and the foods you eat.

Your doctor may do several tests to find the cause of the problem. They include:

Stool test: Too much fat in your stool could mean malabsorption.

Lactose hydrogen breath test: A doctor can see how well you absorb nutrients by measuring how much hydrogen is in your breath after you drink a milk sugar (lactose) solution.

Sweat test: Studying a sample of sweat can help diagnose cystic fibrosis. One of the effects of that disease is a lack of enzymes to properly digest food.

Biopsy of small intestine: A small tissue sample is taken from inside the small intestine and studied to see whether it shows signs of infection or other problems.

Endoscopy: A doctor uses a long, flexible tube with a camera to check out your intestines.

Treatment for malabsorption syndrome depends on the cause.

You may be put on a special diet of foods that are more easily digested and absorbed. You may also be given supplements to make up for nutrients that aren’t being absorbed well.

Sometimes the cause of malabsorption syndrome is an intestinal tract that is too active. Medicines may be prescribed to help it relax and allow more time for nutrients to enter the bloodstream.

If an infection is the cause, you may be prescribed antibiotics.

Malabsorption syndrome can’t always be prevented, especially if you have celiac disease, cystic fibrosis, or other chronic conditions. A chronic condition is one that is ongoing and lasts a long time, from several months to a lifetime.

But you should work closely with your doctor to manage these diseases as much as possible. You should use laxatives and antibiotics carefully and only when necessary.

If you are put on a special diet rich in the nutrients your body needs, be sure to ask your doctor, nurse, or dietitian any questions.