What Is Malabsorption Syndrome?

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The small intestine is part of the digestive system. It finishes breaking down food and absorbs most of the nutrients in food after it passes through the mouth, the esophagus, and the stomach. Malabsorption syndrome develops when your small intestine stops absorbing nutrients properly. It develops after an injury or disease impacts the health of the intestines.

This article covers everything you need to know about the causes, symptoms, diagnosis, and treatment of malabsorption syndrome.

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Possible causes of malabsorption syndrome include:

  • Trauma or injury
  • Bacterial, fungal, viral, or parasitic infections
  • Celiac disease: An autoimmune disease that damages the lining of the small intestine after eating foods containing gluten
  • Inflammatory bowel disease: Conditions that cause inflammation in the intestines, like Crohn’s disease or ulcerative colitis
  • Pancreatitis: Inflammation of the pancreas that can interfere with the release of digestive enzymes
  • Cystic fibrosis: A genetic condition that causes damage to the lungs and digestive system
  • Lactose intolerance: Develops when your body doesn’t produce enough of the enzyme lactase used for digesting the sugar lactose found in dairy products
  • Gallbladder disease: Inflammation or genetic disease impacting the gallbladder, reducing the production and release of bile 
  • Liver disease: Can affect the production of enzymes and bile needed for digestion
  • Long-term antibiotic use
  • Certain medications
  • Small intestinal bacterial overgrowth (SIBO): Occurs when the gut microbiome (the community microbes normally present) in the small intestine is disrupted and impacts digestion
  • Radiation treatment: Malabsorption and digestive problems can be side effects of radiation therapy 
  • Short bowel syndrome (SBS): A rare condition that develops after a large portion of the small intestine is removed during surgery and there is no longer enough small intestine to absorb enough nutrients

Risk Factors

Some of the risk factors for developing malabsorption syndrome include:

  • Family history of cystic fibrosis or digestive diseases
  • Drinking large amounts of alcohol (alcohol use disorder)
  • Surgery on the intestines
  • Use of medications like antibiotics or laxatives
  • Traveling to places with a high risk for intestinal parasites


Depending on the cause of malabsorption syndrome, the symptoms will vary. Some types will only occur after eating a specific food or during flare-ups (when symptoms worsen) of a condition. 

On the other hand, some causes of malabsorption, like short bowel syndrome, lead to long-term digestive changes.

Here are some of the symptoms you may experience with malabsorption syndrome:

  • Frequent diarrhea
  • Gas
  • Bloating
  • Bad smelling, loose stools
  • Oily stool
  • Mucus in stool
  • Light-colored stools
  • Explosive diarrhea
  • Stools that are difficult to flush because they may stick to the sides of the bowl
  • Skin rashes
  • Weight loss
  • Anemia (lack of healthy red blood cells)
  • Low energy and fatigue
  • Dry, brittle hair or nails
  • Hair loss 


If your healthcare provider suspects you have absorption issues, they will likely perform several tests to monitor absorption and find possible causes of malabsorption. Tests used to diagnose malabsorption include:

Stool Test

A sample of stool (feces) is collected to measure fat. Higher than normal amounts of fat in stool often occur in people with malabsorption.

Blood Tests

Blood tests are done to measure the level of nutrients in your bloodstream. 

People with malabsorption syndrome are more likely to experience nutrient deficiencies. As a result, the healthcare provider may order lab work to assess protein, vitamin B12, vitamin D, folate, iron, calcium, and other nutrients.

However, blood work alone can’t diagnose or rule out malabsorption syndrome. Nutrient deficiencies have multiple possible causes. So, even if a test comes back low, it doesn’t necessarily mean you have malabsorption syndrome. 

And a normal lab level doesn’t mean you’re not having absorption problems because it can take time for a deficiency to develop.

Breath Tests

Breath tests measure the amount of hydrogen in your breath after consuming a drink with lactose. These tests are used to diagnose conditions like lactose intolerance and SIBO. 


An endoscopy is a procedure in which a camera attached to a long, flexible tube is used to look at the inside of the intestines.


Imaging tests, like computed tomography (CT) scans or ultrasounds, show the structure of the intestines. They’re used to look for thickening of the intestinal wall and other abnormalities. 


In some cases, your healthcare provider may want to take a sample of your small intestine to assess the health of the cells. Some conditions, like celiac disease, damage the lining of the intestines and can be diagnosed by looking at the cells. 

A biopsy of the small intestine is often done during an endoscopy. 


Treatment for malabsorption syndrome depends on the cause.

Your provider may start by treating any side effects of the malabsorption, like dehydration and nutrient deficiencies. They may begin by replacing fluids and nutrients intravenously (IV).

After replacing some nutrients and fluids, your healthcare provider will look to treat and manage the cause. For example, if you have celiac disease, you’ll need to avoid gluten. For lactose intolerance, you’ll need to avoid most dairy foods.

Your provider may refer you to a registered dietitian to help you make dietary changes to meet your nutritional needs and develop a plan that works for you.

Other treatments that may help malabsorption syndrome include:

  • Digestive enzymes supplements: Digestive enzymes, also called pancreatic enzymes, help your body break down food to support healthy digestion. 
  • Vitamin and mineral supplements: You may be asked to take higher doses of vitamins and minerals to prevent nutrient deficiencies.


If left untreated, malabsorption syndrome may lead to complications like:

  • Vitamin, mineral, protein, or fat deficiencies
  • Interruptions in menstrual cycles or missed periods
  • Stunted or slowed growth
  • Infertility
  • Osteoporosis (low bone density and increased risk for broken bones)
  • Weakened immune system and increased risk of infections


Malabsorption syndrome is a condition in which the small intestine isn’t able to absorb enough nutrients. It can be caused by food allergies, food intolerances, infections, and digestive diseases. Symptoms of malabsorption syndrome include gas, bloating, diarrhea, low energy, light colored stool, and anemia.

It can be diagnosed with stool tests, blood work, breath tests, imaging, or a biopsy. Treatment may include diet changes and supplements. If left untreated, malabsorption syndrome can cause complications like a weak immune system, nutrient deficiencies, and osteoporosis. 

A Word From Verywell 

Most of the time, you can manage malabsorption syndrome with dietary changes and taking supplements to prevent deficiencies. If you think you’re having problems digesting and absorbing food, speak with a healthcare provider to discover the cause and prevent complications. 

You may be asked to follow a special diet to manage malabsorption syndrome. Be sure to talk with your healthcare provider or dietitian if you have any questions. 

Frequently Asked Questions

  • What causes malabsorption syndrome?

    Malabsorption syndrome can be caused by infections, trauma, surgery, and digestive diseases.

  • What is the classic symptom of malabsorption syndrome?

    The most common symptoms of malabsorption syndrome include frequent diarrhea, gas, and bloating.

  • What autoimmune disease causes malabsorption?

    Autoimmune diseases like celiac disease, cystic fibrosis, and Crohn’s disease can cause malabsorption syndrome.

4 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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  2. Semrad CE. Approach to the patient with diarrhea and malabsorption. Goldman’s Cecil Medicine. Published online 2012:895-913. doi: 10.1016/B978-1-4377-1604-7.00142-1

  3. Webb GJ, Brooke R, De Silva AN. Chronic radiation enteritis and malnutritionJ Dig Dis. 2013;14(7):350-357. doi:10.1111/1751-2980.12061

  4. Massironi S, Cavalcoli F, Rausa E, Invernizzi P, Braga M, Vecchi M. Understanding short bowel syndrome: Current status and future perspectives. Dig Liver Dis. 2020;52(3):253-261. doi:10.1016/j.dld.2019.11.013.

By Ashley Braun, MPH, RD
Ashley Braun, MPH, RD, is a registered dietitian and public health professional with over 5 years of experience educating people on health-related topics using evidence-based information. Her experience includes educating on a wide range of conditions, including diabetes, heart disease, HIV, neurological conditions, and more.