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Gastrointestinal malabsorption

Medical Professionals

Professional Reference articles are designed for health professionals to use. They are written by UK doctors and based on research evidence, UK and European Guidelines. You may find the Gastrointestinal malabsorption article more useful, or one of our other health articles.

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What is gastrointestinal malabsorption?

Gastrointestinal malabsorption is a failure to fully absorb nutrients from the gastrointestinal tract. The digestion and absorption of nutrients within the gastrointestinal tract requires a complex interaction between motor, secretory, digestive and absorptive processes that are vulnerable to various potential disturbances which may lead to global or specific malabsorption syndromes.1

The outcome is malnutrition. Malnutrition may also be caused by inadequate diet with or without malabsorption. See also the separate Malnutrition article.

Clinical featuresof gastrointestinal malabsorption2 3

Malabsorption, from whatever cause, may be accompanied by:

There may also be clinical features associated with the particular cause of malabsorption. The most common causes in the UK are coeliac disease, Crohn's disease and chronic pancreatitis.

However the malabsorption of simple carbohydrates is the most common type of non-immune-mediated food intolerance, affecting 20-30% of the European population4 .

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Various causes of gastrointestinal malabsorption2 5

Mucosal causes

Intraluminal causes

Structural causes

Causes outside the gut

Investigations3 5 11

Blood tests

  • FBC.

  • Plasma viscosity, ESR, CRP.

  • Vitamin B12 level.

  • Red cell folate.

  • Iron status (usually ferritin but can be iron and iron-binding capacity).

  • Clotting screen for vitamin K deficiency.

  • Serum albumin.

  • Calcium (corrected for albumin level).

  • Magnesium, zinc, phosphorous.

  • Vitamin D.

  • Anti-endomysial, anti-reticulin and alpha-gliadin antibodies (coeliac screen).

  • LFTs.


  • Faecal microbiological assessments may be indicated.

  • Sudan stain for fat globules.

  • Tests for secretory function - eg, elastase or chymotrypsin in stool.

Imaging and endoscopy

  • Abdominal ultrasound (gallbladder, liver, pancreas, intestinal wall, adenopathy).

  • Barium follow-through may show structural abnormalities.

  • Jejunal biopsy (and aspirate for possibility of SIBO).

  • Ileocolonoscopy including biopsies of colon and ileum.

  • CT; MRI of pancreatic duct-systems or endoscopic retrograde cholangiopancreatography (ERCP).

Breath hydrogen tests

Take samples of end-expired air; give glucose; take more samples at half-hourly intervals. If there is bacterial overgrowth there is an increase in exhaled hydrogen one hour after ingestion.

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Gastrointestinal malabsorption treatment and management2 3 5

Nutritional support may be required for malabsorption.

Management otherwise depends upon the cause. For example:

  • Coeliac disease requires a strict gluten-free diet.

  • Pancreatic insufficiency requires the oral administration of enzymes with food.

  • Blockage of the flow of bile requires surgery.

  • Crohn's disease usually responds to steroids.

  • Blind loop syndromes may require further surgery.

  • Where bile salts are not reabsorbed, it may be necessary to give resins to bind them.12

  • If there is folate deficiency and possibly B12 deficiency too, it is imperative to give an injection of vitamin B12 before starting folate supplementation. Otherwise, there is a risk of precipitating subacute combined degeneration of the cord.

Malabsorption complications

Complications are related to the underlying disease.

  • Lassitude is common. Children will have stunted growth.

  • Untreated coeliac disease may result in small bowel adenocarcinoma or lymphoma.

  • Infertility is common, especially in coeliac disease.

  • Anaemia may occur.

  • Rickets, osteomalacia or osteoporosis may occur.

Further reading and references

  1. Keller J, Layer P; The Pathophysiology of Malabsorption. Viszeralmedizin. 2014 Jun;30(3):150-4. doi: 10.1159/000364794.
  2. Davis J, Kellerman R; Gastrointestinal Conditions: Malabsorption Syndromes. FP Essent. 2022 May;516:31-37.
  3. Ghoshal UC, Mehrotra M, Kumar S, et al; Spectrum of malabsorption syndrome among adults & factors differentiating celiac disease & tropical malabsorption. Indian J Med Res. 2012 Sep;136(3):451-9.
  4. Raithel M, Weidenhiller M, Hagel AF, et al; The malabsorption of commonly occurring mono and disaccharides: levels of investigation and differential diagnoses. Dtsch Arztebl Int. 2013 Nov 15;110(46):775-82. doi: 10.3238/arztebl.2013.0775.
  5. Burgers K, Lindberg B, Bevis ZJ; Chronic Diarrhea in Adults: Evaluation and Differential Diagnosis. Am Fam Physician. 2020 Apr 15;101(8):472-480.
  6. Latulippe ME, Skoog SM; Fructose malabsorption and intolerance: effects of fructose with and without simultaneous glucose ingestion. Crit Rev Food Sci Nutr. 2011 Aug;51(7):583-92. doi: 10.1080/10408398.2011.566646.
  7. Agarwal S, Mayer L; Gastrointestinal manifestations in primary immune disorders. Inflamm Bowel Dis. 2010 Apr;16(4):703-11. doi: 10.1002/ibd.21040.
  8. Murray JA, Rubio-Tapia A; Diarrhoea due to small bowel diseases. Best Pract Res Clin Gastroenterol. 2012 Oct;26(5):581-600. doi: 10.1016/j.bpg.2012.11.013.
  9. Hackert T, Schutte K, Malfertheiner P; The Pancreas: Causes for Malabsorption. Viszeralmedizin. 2014 Jun;30(3):190-7. doi: 10.1159/000363778.
  10. Achufusi TGO, Sharma A, Zamora EA, et al; Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods. Cureus. 2020 Jun 27;12(6):e8860. doi: 10.7759/cureus.8860.
  11. Ensari A; The Malabsorption Syndrome and Its Causes and Consequences. Pathobiology of Human Disease. 2014 : 1266–1287.
  12. Johnston I, Nolan J, Pattni SS, et al; New insights into bile acid malabsorption. Curr Gastroenterol Rep. 2011 Oct;13(5):418-25. doi: 10.1007/s11894-011-0219-3.

Article History

The information on this page is written and peer reviewed by qualified clinicians.

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