Malabsorption : Medical guide to causes, diagnosis & treatment

Read more to know what causes this problem, symptoms & signs you would see if you are having such defect, what happens if untreated and how to detect and treat.

Are you having Diarrhoea and weight loss despite of having a normal diet? Are you excreting a pale bulky stool that is having an offensive odour? This may be due to Malabsorption syndrome.

You have malabsorption when there is a defect in absorption of nutrients leading to their deficiencies that further results in myriad of signs and symptoms.

These nutrients include Carbohydrates, Vitamins, Fats, Proteins and minerals and trace elements.

Read more to know what causes this problem, symptoms & signs you would see if you are having such defect, what happens if untreated, how to detect and treat.

What is Malabsorption?

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Malabsorption is said when the food is not getting absorbed which may be due to defect in the absorptive surface or defect in the enzymes and Bile or a defect in the lymphatics that take up the absorbed nutrients and distribute it into the systemic circulation.

The whole process of food intake upto removal is divided into 5 steps:

  • Ingestion : It involves taking in a substance through the mouth into the gastrointestinal tract; such as through eating or drinking.
  • Digestion : It is the process of breaking down of large insoluble food you eat into small water soluble nutrients so that they can be absorbed into the watery blood plasma.
  • Absorption : The small water soluble food or nutrients pass through the wall of the small intestine and into your bloodstream. Once there, the digested food molecules are carried around the body to where they are needed.
  • Assimilation :The absorbed food materials are transported by blood and lymph to the cells of the body where they are used.
  • Excretion : The food that remains undigested and unabsorbed are passed down and removed out of the body.

The step that is involved in absorption is the main culprit. This leads to deficiency of carbohydrates, fats, proteins, vitamins and minerals in the body leading to clinical features that are diverse in nature and variable in severity.

What causes Malabsorption?

For the nutrients to get absorbed properly, it usually requires normal bile synthesis & transport, pancreas, intact small intestinal absorptive surface and lymphatics to deliver the absorbed nutrients into systemic circulation.

If any of the above gets impaired, there could be defective absorption leading to clinical feature that you will find below in this article.

Let us see what are the common causes of malabsorption…

Abnormal digestion in the lumen of gastrointestinal tract resulting from

Liver Cirrhosis

Liver is responsible for formation of bile acids. Bile acids are important for the absorption of fat by forming micelles. In cirrhosis, liver cells (hepatocytes) are unable to form bile acids leading to fat malabsorption.

Bile Duct defect

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Bile acids reach small intestine through bile duct. If there is a problem in bile duct, bile acids won’t be able to reach small intestine to help absorb fat. This problem could be due to:

  • Primary Biliary Cirrhosis :It is an autoimmune destruction of intrahepatic bile duct.
  • Primary Sclerosing Cholangitis: It involves fibrosis of Intrahepatic and extrahepatic bile duct.

Overgrowth of bacteria in small intestine

A large number of bacteria are usually found in Large Intestine. These bacteria in colon (a part of large intestine) deconjugates bile acids after their use.

When these bacteria overgrow in small intestine, they tend to deconjugate bile acids even before their use (only conjugated bile acids are needed for absorption).

Ileal disease

A disease of Ileum (A part of small intestine) where there is a defective entero-hepatic circulation (A circulatory pathways responsible for transport of used bile acids back to bile acid pool in liver. This defect may be seen in :

  • Crohn’s Disease
  • Intestinal Tuberculosis

Disease of Pancreas

Pancreas releases important enzymes (Trypsin, chymotrypsin, carboxypeptidase) that is responsible for breakdown of large insoluble food into small water soluble nutrients that are easily absorbable. These enzymes are not released when there is a diseased pancreas like in Chronic Pancreatitis.

Defect in mucosa of small intestine

It diminishes the surface area for absorption and depletes the brush border enzymatic activity. This is seen in case of:

  • Celiac disease
  • Whipple disease
  • Tropical sprue
  • Short Bowel syndrome
  • Abetalipoproteinaemia

Obstruction of Post-mucosal lymphatics

This prevents the uptake and transport of absorbed lipids into lymphatic vessels.
Seen in case of Intestinal Lymphangiectasia.

Malabsorption is also associated with:

  • Lactose Intolerance
  • Hartnup disease
  • Cystinuria
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Now you know what causes it, you must also know what happens to you if you have malabsorption.

What are the signs & symptoms of Malabsorption?

Since it could lead to a deficiency of carbohydrates, fats, proteins, vitamins, minerals & trace elements, the symptoms are diverse in nature and variable in severity.

The clinical features are not just limited to gastrointestinal tract but also involves musculo-skeletal system, cutaneous and other systems.

Following are the clinical features you would likely be seeing in case of malabsorption :

Gastro-intestinal symptoms:

  • Diarrhoea
  • Abdominal distention
  • Abdominal discomfort
  • Bulky, pale and foul smelling stool that float in the toilet (Steatorrhoea)
  • Rumbling sounds from the stomach or intestine (Borborygmi)
  • Abdominal cramps
  • Undigested food in the stool

Musculoskeletal symptoms:

  • Bone pain
  • Fracture
  • Tetany : Involuntary contraction of muscles.
  • Paraesthesia : When you have an abnormal sensation, typically tingling or pricking with no apparent physical cause.
  • Osteomalacia : When you have weak or soft bones basically happens due to vitamin D deficiency.
  • Muscle weakness : When you have a deficiency of calcium, magnesium and phosphorus.

Cutaneous manifestations:

  • Easy bruisability – Due to vitamin K deficiency.
  • Ecchymosis – Due to vitamin K deficiency.
  • Follicular hyperkeratosis – Due to vitamin A deficiency.
  • Acrodermatitis Enteropathica – Due to Zinc deficiency.
  • Hyperpigmented Dermatitis – Due to deficiency of Niacin.
  • Peri-follicular Haemorrhage -Due to deficiency of vitamin C.

CNS & EYE features:

  • Neuropathy
  • Ataxia
  • Night blindness
  • Lethargy
  • Depression

Malabsorption can also lead to:

  • Weight loss
  • Fatiguability
  • Edema
  • Ascites
  • Muscle wasting
  • Anemia
  • Clubbing
  • Oxalate stones in kidney
  • Bleeding gums
  • Poor wound healing

How to confirm malabsorption?

Your are likely to have malabsorption if you are having diarrhoea and weight loss with a normal diet. You will then be considered as a suspected case of malabsorption and certain tests will be used to confirm the diagnosis. These tests include:

Blood test

Blood samples are collected and level of specific substances in blood are measured. These substances include urea, electrolytes, immunoglobulins, calcium, magnesium, albumin, clotting factors, folate, iron, vitamins, coeliac antibodies etc..

Stool test

Your stool sample is collected to check for the presence of fat, specific proteins and enzymes in the stool or faeces and measure the amount of the same.

Presence of pale, bulky and foul smelling stool is the hallmark of malabsorption. Tests done on the stool samples include :

  • 72 hour fecal fat test :This is the best test to measure the amount of fat in your stool sample.
  • Acid steatocrit test : The test is simple, rapid, inexpensive, and reliable to measure the fat content in stool sample. It is a more convenient alternative to the 72 hour faecal fat test as it requires only a single stool sample.
  • Stool fat by sudan III stain : It is a quick and simple test to test for the presence of fat in stool sample.
  • Fecal calprotectin test : It is a test used to detect inflammation in the intestine. Calprotectin is a protein secreted non-specifically by neutrophils into the colon in response to inflammation or neoplasia.
  • Stool Chymotrypsin and Elastase : Deficiency of these enzymes indicate insufficient pancreas and protein malabsorption.

Breath test

Lactose H2 Breath test

It is used to test for the presence of lactose intolerance.

If you have malabsorption, lactose instead of getting absorbed through small intestion will reach colon. The bacteria in colon break down the lactose and produce Hydrogen gas. The intestine absorbs hydrogen which are in excess and transfers it to your blood stream and then to your lungs. You will exhale this hydrogen which will be detected by the test.

If hydrogen gas is found to be in your breath after your intake of products containing lactose, you may have lactose intolerance.

13C egg white breath test

It is a non-invasive test to check for protein malabsorption. It basically tests for pancreatic trypsin enzyme activity in small intestine.

14C triolein breath test

It is used to investigate the absorption of fats from the small bowel.

Urine test

Your urine samples may also be collected to detect certain substances. The amount of specific substances are measured and checked whether there is deviation from the normal. The tests done on urine samples include :

Urine d-xylose test

It is the best non-invasive test for carbohydrate malabsorption.

Xylose is a carbohydrate that requires only an intact small intenstinal mucosa for its absorption. If there is an intestinal mucosal disease, xylose won’t get absorbed and reach system circulation and therefore, its level will decrease in urine.

You are given 25g of D-Xylose. If its urinary excretion is more than 4.5-5g, the mucosa of small intestine is intact. If the level in urine sample is found to be less than 4.5g-5g, it indicates an intestinal mucosal disease.

Test for Bile salt malabsorption

As we have said above, Bile acids and bile salts plays an important role in absorption of fat and after their purpose gets served, they return to liver to maintain bile acid pool.
Malabsorption of bile salts may lead to their deficiency resulting in fat malabsorption and bile acid diarrhoea eventually.

Your doctor does certain tests to look for abnormalities in Bile acid absorption and return to liver. These tests include :

75SeHCAT test

The 75-selenium homocholic acid taurine (SeHCATtest is a nuclear medicine investigation considered to be the gold standard for the diagnosis of bile acid malabsorption.

It is a diagnostic procedure to determine how well your gut is able to absorb bile acids. It requires two appointments 1 week apart.

On your first appointment you will be asked to swallow a small SeHCAT capsule with a glass of water. A scan will then be undertaken three hours later. This scan will take approximately 20 minutes.

On your second appointment you will only have a scan which again will take approximately 20 minutes.
The amount of bile acid remaining after the second scan will determine whether or not you have Bile Salt Malabsorption.

Serum 7-alpha-hydroxycholestenone test

Serum 7-alpha-hydroxycholestenone is an intermediate metabolite of the bile acid synthetic pathway.
Serum levels indicate activity of the pathway and are elevated in bile acid diarrhoea.

It is a simple test to perform and only marginally less sensitive and specific that SeHCAT test.


Your doctor will take a tissue specimen from the mucosa of your small intestine and will check for any abnormalities microscopically.

It is useful for detecting defects in the absorptive surface of small intestine that could be due to celiac disease, whipple’s disease, tropical sprue, abetalipoproteinemia, agammaglobulinemia etc.

Biopsy is usually done using endoscopy. You doctor puts a flexible tube through mouth into your intestine and takes tissue samples from the intestinal mucos.

Imaging studies

Imaging of your gastrointestinal tract basically means taking a pictureof it especially to check for any structural abnormalities. These tests include :

Barium studies

Barium Follow through test is done to look for problems in small intestine.

You drink the barium liquid but then need to wait 10-15 minutes before any X-rays are taken. This allows time for the barium to reach the small intestine. You may then have an X-ray every 30 minutes or so until the barium is seen to have gone through all the small intestine and reached the large intestine (colon).

Small bowel MRI

Small bowel magnetic resonance imaging is useful in detecting inflammation in small intestine like as in Crohn’s disease.

It has an advantage over other studies as it has a lak of radiation exposure, good soft tissue contrast and repeated data acquisition for functional bowel evaluation.

MRI uses a very strong magnet to give detailed images of your bowel. A liquid mixture is given to you to drink to fill the small bowel so that it can be seen well on the scan.

Ultrasound Scan

Intestinal ultrasound is a safe, easily accessible, non-invasive, radiation-free, and cheap method that allows visualisation of the gastrointestinal tract and detection of abnormalities.
Advantages of ultrasound are availability and cost.

It is a promising method with high sensitivity and specificity, which has gained popularity in recent years and has the potential to become the method of choice in the diagnostics of many intestinal disorders.

CT Scan

Computed Tomography of small bowel is used to find out what may be causing your symptoms (e.g. weight loss, diarrhoea, abdominal pain etc). It involves drinking a fluid to fill the small bowel. You will then have a CT Scan of your abdomen and pelvis.

A CT Scanner is an open, ring shaped machine which uses X-ray to take detailed pictures in ‘thin slice sections’.

How malabsorption is treated?

If you are diagnosed of having malabsorption syndrome, you need to get treated to prevent severe complictions. Treatment in the setting of malabsorption syndromes targets correcting deficiencies, treating the underlying cause, avoiding triggers (typically dietary), and treating symptoms (e,g often diarrhea).

Treatment could be as conservative as dietary changes such as food avoidance or supplementation but could be as invasive as surgery.

For Lactose intolerance

  • Avoidance of dairy products.
  • Lactase supplementation.

Vitamin supplementation

This is advised by the doctors to prevent developing defeciency of essential vitamins in the body.

Dietary changes

Changes in diet is advised according to the clinical features that tend to develop. For instance, high fat diet should be avoided in case of diarrhoea and increasing certain electrolytes in food with respect to their serum levels.

Assessing and improving nutrition status should be included in any treatment plan regardless of diagnosis.

Endoscopic retrograde cholangiopancreatography (ERCP)

This could be curative when removing an obstructing stone in pancreatitis.

Pancreatic enzyme replacement

This would be indicated in case of pancreatic exocrine insufficiency that means when pancreatic enzymes are not being released for the proper digestion of food.

It is important to note that antibiotics could be the cause of a patient’s diarrhoea or the cure if due to a bacterial infectious process.

Differential Diagnosis for malabsorption syndrome

A differential diagnosis is a list of probable disorders with similar signs and symptoms.

Some differentials are specific to a malabsorption syndrome or presenting symptom. Following are the probable disorders that could cause similar clinical features with that of malabsorption:

  • Constrictive Pericarditis
  • Crohn’s disease
  • Systemic sclerosis
  • Whipple’s disease
  • Intestinal Tuberculosis
  • Sarcoidosis
  • Cystic Fibrosis
  • Congenital chloride malabsorption
  • Congenital glucose-galactose malabsorption
  • Pancreatic insufficiency

Outcome of malabsorption syndrome

Typically, malabsorption syndrome is not life threatening. However, with some conditions, its severity and duration can be lethal. Such dangerous conditions include:

  • Severe malnutrition from prolonged pancreatic exocrine insufficiency
  • Life-threatening electrolyte disturbances from prolonged, intractable diarrhea
  • Bowel perforation

In case of lactose intolerance, deterioration of health is unlikely to happen.

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Abhinav is currently working as an Intern doctor. Being an avid reader by day and a freelance writer by night, he has been much active among medical students since past few years. Support him on his journey of being a Medical Influencer.


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