Malabsorption Syndrome Overview

Malabsorption – the failure to completely absorb nutrients from the gastrointestinal tract – is an enormous health care problem in the United States today.

The list of causes, signs, symptoms, clinical features, and complications of malabsorption is so long, it’s practically mind-boggling. The causes alone total over two hundred!

Many serious illnesses are linked to malabsorption. For example, Celiac disease is the most common inherited malabsorption syndrome.

The prevalence of Celiac disease alone is approximately 1% of the general population of the United States, and the numbers have been increasing over time.

But what, exactly, is malabsorption, and what – if anything – can be done to protect yourself from this syndrome?

Malabsorption Syndrome

How Malabsorption Works Against Good Digestive Health

Rather than being one specific disorder, malabsorption includes a number of conditions whereby food nutrients are not adequately absorbed in the small intestine.

To prevent and/or alleviate the symptoms and resulting complications of malabsorption, it’s important to understand what happens (or does not happen) when this condition sets in.

In a person with a healthy digestive system, food is eaten and digested, and nutrients are absorbed into the bloodstream in the small intestine. If a disorder disrupts the digestion of food, or directly interferes with nutrient absorption, malabsorption becomes a potential factor.

Various substances are necessary for healthy digestion to take place. Conditions that prevent sufficient mixing of food with substances such as digestive enzymes and hydrochloric acid (HCl) in the stomach can seriously affect digestion. This can happen to patients who’ve had a part of their stomach surgically removed.

For people with other types of disorders, adequate amounts or types of digestive enzymes don’t get produced. Insufficient bile or pancreatic enzyme production, an abundance of HCl, or too many bad bacteria growing in the small intestine may also negatively affect digestion.

Types of Malabsorption

While malabsorption can involve a general inability to absorb food, it is predominantly the inability to absorb certain sugars, fats, proteins, or vitamins from food.

There are three basic categories of malabsorption:

  1. Selective, as with lactose malabsorption
  2. Partial, as observed in those with abetalipoproteinemia (an inherited disorder that affects the absorption of dietary fats, cholesterol, and fat-soluble vitamins)
  3. Total, as in the case of those with Celiac disease

Within these categories, there are many specific types:

  1. Sugar malabsorption: usually of lactose or milk sugar, is the most common form of malabsorption.
  2. Fat malabsorption: a more serious health concern than sugar malabsorption, necessitates an evaluation of the bile ducts, pancreas, and small intestine. This can also result in deficiencies of the fat soluble vitamins A, D, E, and K.
  3. Nutrient malabsorption: several distinct malabsorption conditions affect the various steps in the transportation of nutrients. For example, iron deficiency anemia – resulting from iron malabsorption by the small intestine – is often caused by Celiac disease.

What Causes Malabsorption?

Nutrient absorption can be caused by disorders that have injured the lining of the small intestine. Comprised of villi and microvilli (tiny and even smaller finger-like projections of membrane), healthy intestinal lining provides a huge surface area for absorption.

Surgical removal of part of the small intestine (intestinal resection) reduces the surface area for absorption (short bowel syndrome).

Acute, abnormal intestinal lining resulting from bacterial, parasitic, or viral infections; alcohol and certain drugs (antibiotics); and chronically abnormal intestinal lining resulting from injurious diseases such as Celiac and Crohn’s can also be causes of malabsorption.

Disorders that affect the remaining layers of the intestinal wall also inhibit absorption.

The two hundred causes can be classified into four distinct categories:

  1. Those relating to the mucous membranes (mucosal) such as cow’s milk intolerance.
  2. Intraluminal, that is, causes relating to the cavity of the intestine such as chronic pancreatitis.
  3. Structural, for example Crohn’s disease.
  4. Causes outside the gut, such as eating disorders (lack of substrate to absorb).

Here is a list of some of the causes of malabsorption, by category:

1. Mucosal Causes

  • AIDS (Acquired Immune Deficiency Syndrome)
  • Celiac disease
  • Cow’s milk protein intolerance
  • Giardia lamblia / giardiasis
  • Hookworm and roundworm infection
  • Intestinal tuberculosis
  • Intestinal lymphectasia (and other causes of lymphatic obstruction include lymphoma, tuberculosis and cardiac disease)
  • Soy milk protein intolerance
  • Traveler’s diarrhea
  • Tropical sprue
  • Whipple disease

2. Causes Outside the Gut

  • Addison’s disease
  • Carcinoid syndrome
  • Diabetes
  • Eating disorders
  • Hyperparathyroidism
  • Hyperthyroidism
  • Hypoparathyroidism
  • Hypothyroidism
  • Malnutrition

3. Structural Causes

  • Amyloidosis (protein builds up in the organs and tissues)
  • Certain surgeries (gastrectomy, gastric bypass, etc.)
  • Crohn’s disease (Can Crohn’s Kill You)
  • Diverticulae and strictures
  • Eosinophilic gastroenteritis
  • Fistulae
  • Mesenteric arterial insufficiency
  • Parasites
  • Radiation treatment damage
  • Short bowel syndrome

4. Intraluminal Causes

  • Chronic pancreatitis
  • Cystic fibrosis
  • Defective bile salt secretion
  • Zollinger-Ellison syndrome

5. Other Causes

  • Abetalipoproteinemia (an inherited disorder affecting absorption of dietary fats, cholesterol, and fat-soluble vitamins)
  • Biliary atresia (a rare condition in newborns whereby the common bile duct between the liver and small intestine is blocked or absent)
  • Certain medications (some antacids, antibiotics, and medications for obesity)
  • Certain cancers (lymphoma, pancreatic cancer, gastrinomas)
  • Cholestasis (a condition whereby bile cannot flow from the liver to the duodenum)
  • Chronic liver disease / PSC
  • Collagen diseases
  • Lactose intolerance
  • Pernicious anemia
Malabsorption Syndrome

Symptoms of Malabsorption

Malabsorption signs and symptoms vary depending on the specific deficiency.

Poor protein absorption, for example, can present with bodily swelling, dry skin, and hair loss. Insufficient absorption of specific sugars can result in abdominal bloating, diarrhea, and severe flatulence.

Inadequate absorption of fats in the digestive tract can result in stool that is oily, greasy, fluffy, soft, and foul smelling (a condition known as steatorrhea).

Signs of malabsorption may include one or more of the following:

  • Abdominal pain
  • Anemia
  • Bleeding
  • Bloating in Upper Abdomen
  • Bulky stools
  • Changes in weight and growth
  • Cramping
  • Dehydration
  • Diarrhea
  • Failure to thrive in children
  • Fatigue
  • Flatulence
  • Folate deficiency
  • Gas
  • Iron deficiency with or without anemia
  • Lethargy
  • Muscle wasting
  • Oily stools
  • Skin changes
  • Steatorrhoea
  • Undigested food in stool
  • Vitamin B12 deficiency

Malabsorption can also affect growth and development, and lead to certain illnesses.

Malabsorption Related Illnesses

Long-term malabsorption can result in:

  • Anemia
  • Gallstones
  • Heart failure
  • Kidney stones
  • Malnutrition
  • Osteoporosis and osteomalacia (bone disease)

Further malabsorption complications include infertility, rickets, and stunted growth in children. In addition, untreated Celiac disease can lead to small bowel cancer or intestinal lymphoma.

Diagnosing Malabsorption

When a patient is suffering with chronic diarrhea, nutritional deficiencies, and substantial weight loss despite a healthy diet, their doctor may suspect malabsorption.

More difficult to diagnose in older people than in the young, a variety of diagnostic tests are available to help make a determination.

Laboratory tests

Along with a complete physical exam, various other tests may be necessary to make an accurate diagnosis of malabsorption:

A complete blood count (CBC) can determine whether or not anemia is the cause for malabsorption.

Iron levels, vitamin B12 level, red cell folate (folic acid), and clotting factors (which can be abnormal with vitamin K deficiency) are measured. In addition, specific antibody screens can detect Celiac disease.

Serum electrolytes can determine whether or not electrolyte imbalances – such as low levels of calcium, potassium, or magnesium – have developed as a result of malabsorption.

Liver function tests are performed to detect, evaluate, and monitor liver disease or damage.

Pancreatic function tests (blood tests) measure the gland’s ability to secrete an adequate supply of enzymes or other substances necessary for digestion.

Amylase (the pancreatic enzyme responsible for digesting carbohydrates), lipase (the enzyme that digests fats), and trypsin (which digests proteins) levels are measured to determine pancreatic sufficiency.

Stool studies, the collection of stool samples over a two- or three-day period, is one of the most dependable ways to make a fat malabsorption diagnosis. More than seven grams of fat per day in the stool is a distinguishing malabsorption feature.

Stool pancreatic elastase is a marker of fat malabsorption that is less burdensome to collect, requiring a one time sample, rather than 3 day stool collection.

Stool can also be assessed for parasites or their eggs since a parasitic infection may be the cause of malabsorption. Learn more in this article: Parasitic Feeders.

Hydrogen breath tests examine samples of expired air for bacterial overgrowth by measuring exhaled hydrogen and/or methane after a sugar is consumed by the patient.  These can also be used to assess for malabsorption of lactose, sucrose and fructose.

Secretin stimulation tests examine the pancreas’ ability to respond to the hormone secretin, produced by the small intestine when partially digested food has moved from the stomach to the beginning of the small intestine.

Radiographic tests

X-rays with barium liquid contrast require a chalky solution, barium, to be drunk to coat the lining of the small intestine. Barium appears white on X-ray film, revealing any structural abnormalities, like strictures of fistulae. 

Computerized tomography scans (CT scan) is a specialized X-ray technique capable of collecting more detail than a standard X-ray. CT scans can determine whether or not there is an underlying illness such as chronic pancreatitis or Crohn’s disease for which malabsorption has become a symptom and/or complication.

Endoscopic retrograde cholangiopancreatography (ERCP) combines the use of X-rays and an endoscope to examine the liver’s bile ducts and pancreatic duct (biliary tree assessment).

Under sedation, a small tube is inserted down the throat into the duodenum. A dye is injected into the duct, and an X-ray is taken.  

Endoscopic ultrasound can also evaluate this anatomy using an endoscope with an ultrasound probe inserted into the stomach. This does require anesthesia but avoids radiation.


Endoscopic tests for specific sections of the gastrointestinal (GI) tract are sometimes used to do a visual exam.  All use a thin, flexible tube with a lighted camera inside the tip which enables a visual exam of the GI tract lining.

A biopsy – the taking of a tissue sample from the intestinal lining to be used for further examination – may be required to detect abnormalities in the small intestine’s lining. The tissue is removed and sent to a pathologist for an exam under a microscope.

Preventing Malabsorption

Since many malabsorption syndromes are hereditary, genetic screening may help prevent passing on the syndrome to unborn children. Early detection for infants and children is one of the best preventatives for hereditary malabsorption.

For some people, prevention of malabsorption syndromes can be as simple as avoiding foods or other substances (such as impure/unfiltered water sources while traveling or certain medications) that produce gastrointestinal distress or infections.

Subsequent monitoring to prevent additional nutritional deficiency illnesses is indicated.

Sometimes, a specific food can cancel out the effectiveness of a prescribed medication due to changes in absorption, leading to serious health problems over the long-term.

For example, grapefruit juice reacts with various drugs causing potentially dangerous side effects. Lipitor (for lowering cholesterol) if taken with recently ingested grapefruit or its juice may result in muscle cramps.

Note any changes in your overall health. For example, muscle cramps and bone pain may indicate a vitamin D deficiency. 

Malabsorption Syndrome Treatment

Prognosis depends on the underlying condition that is causing malabsorption. But much can be achieved – such as alleviating symptoms and decreasing the likelihood of further illness – through lifestyle changes, probiotics, and vitamin and nutrient supplementation.

A few basic treatment principles apply to nearly all malabsorption cases:

  • Prescription medications, like antibiotics for a bacterial infection or anti-inflammatories for Crohn’s disease, can treat the underlying condition and reduce malabsorption.
  • Avoid foods that seem difficult to digest – lactose, gluten, soy, shellfish, eggs, and nuts are common culprits.
  • Consider taking enzyme fortified drinks and supplements.
  • Drink lots of water to help flush out the system, and assist in effective kidney function
  • Replace lost nutrients with a variety of foods including fresh fruits, vegetables and lean meats
  • Take a multivitamin to help make up any deficiencies from the diet
  • Take a probiotic which may help increase the absorption of trace minerals, especially in people with high-phyate diets (i.e. legumes, nuts, and whole grains)

Malabsorption Syndrome Final Thoughts

Many serious illnesses are linked to malabsorption. An inflamed ileum (such as with Crohn’s disease) can interfere with the absorption of vitamin B12 and bile salts.

Any inflammation along the length of the small intestine will seriously impair the absorption of all food.

Prognosis greatly depends upon the underlying condition causing malabsorption.

But the implementation of a prevention and treatment regimen including probiotics, and vitamin and nutrient supplementation can substantially alleviate symptoms, and prevent the onset of many more serious complications.

You might be interested in these other gastrointestinal conditions:

Written and Medically Reviewed By

  • Sheila Jennings

    Sheila Jennings is a 4th-year medical student and also freelances as a content writer on gut health, nutrition, and food. She lives with IBS and has learned how to keep her symptoms at bay through a healthy diet and exercise. She wants to educate others on what they can do to take back control of their gut health and live like they used to.

  • Julie Guider, M.D.

    Dr. Julie Guider earned her medical degree from Louisiana State University School of Medicine. She completed residency in internal medicine at the University of Virginia. She completed her general gastroenterology and advanced endoscopy fellowships at University of Texas-Houston. She is a member of several national GI societies including the AGA, ACG, and ASGE as well as state and local medical societies.