Malabsorption is characterized by the inability to digest or absorb nutrients from the small intestine into the bloodstream and is related to diseases of the pancreas, liver, and intestine. Test choice depends on the clinician’s suspicion regarding the etiology of the malabsorption (eg, carbohydrate malabsorption versus fat malabsorption). “Shotgun” approaches to malabsorption evaluations are not recommended.

  • Key Points
  • Diagnosis
  • Algorithms
  • Background
  • Lab Tests
  • References
  • Related Topics
Primary Authors: Couturier, Marc Roger, PhD, D(ABMM). Grenache, David G., PhD.

Diarrhea is a common complaint in malabsorptive disorders. Multiple tests are available for evaluating malabsorption; some are more sensitive than others.

Indications for Testing

  • Chronic diarrhea, steatorrhea, or preexisting condition that may predispose to malabsorption

Laboratory Testing

  • Initial nonspecific screening tests
  • Specific tests
    • TSH – rule out thyroid disease
    • Cystic fibrosis testing (sweat chloride)
    • Initial fecal tests – perform in parallel with serum tests
    • Consider celiac testing (tTG antibody testing with IgA level)
    • Stool culture, ova and parasite – evaluation using GI panels; C. difficile testing if risk factors present
      • Fecal leukocytes – present in IBD, infectious diarrhea
      • Fecal occult blood
      • Fecal fat, qualitative/quantitative
  • Secondary testing
    • Based on clinical history and above test results
    • Refer to Key Points section

Imaging Studies

  • If initial test results are normal, consider abdominal CT or ultrasound, endoscopy

Differential Diagnosis

  • Refer to causes of malabsorption in Clinical Background section

Causes of Malabsorption

  • Inadequate digestion of nutrients
  • Inadequate absorption of nutrients
    • Shortened bowel or loss of absorptive surface (eg, inflammatory bowel disease [IBD], including ulcerative colitis, Crohn disease, gluten-sensitive enteropathy [Celiac sprue], tropical sprue, lymphoma, surgical loss of functional bowel, blind-loop syndrome, hormonal disorders)
    • Impaired nutrient metabolism (eg, deficiency of intestinal disaccharidases, lactase deficiency)
    • Nutrient-specific transport deficiencies (eg, Hartnup disease)
    • Decreased availability of specific nutrients (eg, vitamin B12 deficiency due to decreased intrinsic factor)
    • Alterations of circulation (eg, mesenteric ischemia, heart failure, portal hypertension, lymphatic obstruction
  • Miscellaneous


  • Nutrient digestion and absorption occur in three phases
    • Luminal phase – breakdown and solubilization of proteins, carbohydrates, and fats by digestive enzymes and bile
    • Mucosal phase – transport of digested nutrients into gastrointestinal epithelial cells
    • Transport phase – transport of nutrients via lymphatics and portal circulation from small intestine to other parts of the body
  • Any process that disrupts one or more of these phases can cause malabsorption

Clinical Presentation

  • Prominent symptom – chronic diarrhea
  • Constitutional – weight loss, fatigue
  • Gastrointestinal – steatorrhea, abdominal bloating, abdominal pain, somatostatinoma
  • Extraintestinal – anemia, skin rashes, stomatitis, glossitis, peripheral edema, ascites
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Occult Blood, Fecal by Immunoassay 2007190
Method: Quantitative Immunoassay

Lactoferrin, Fecal by ELISA 0061164
Method: Qualitative Enzyme-Linked Immunosorbent Assay

Calprotectin, Fecal 0092303
Method: Quantitative Enzyme-Linked Immunosorbent Assay

Gastrointestinal Parasite Panel by PCR 2011150
Method: Qualitative Polymerase Chain Reaction


Due to periodic shedding of some parasites, a result of “not detected” cannot completely rule out infection with these parasites

If clinical signs and symptoms persist, an additional specimen for testing may be indicated

Viral and bacterial gastroenteritis are more common than parasite gastroenteritis and should be considered as alternative diagnoses

Asymptomatic infections are known to occur and, therefore, correlation of test results with clinical signs and symptoms is imperative

Panel does not detect

  • Helminths (flatworms, roundworms, and flukes)
  • Nonpathogenic protozoa
  • Cystoisospora
  • Microsporidia

​Negative result does not rule out presence of PCR inhibitors in specimen or assay-specific nucleic acid in concentrations below the level of detection

Gastrointestinal Bacterial Panel by PCR 2012678
Method: Qualitative Polymerase Chain Reaction


Negative result does not rule out presence of PCR inhibitors in the patient specimen, test-specific nucleic acid in concentrations below the level of detection

Molecular assays will not detect rare or unusual enteric bacterial pathogens that are not specifically targeted by the test (eg, Aeromonas, Plesiomonas, Yersinia, Vibrio, and enterotoxigenic E. coli)

A bacterial isolate is not obtained if antimicrobial susceptibility testing is indicated

Disaccharidase, Tissue 2002247
Method: Quantitative Spectrophotometry

Reducing Substances, Fecal 0020373
Method: Semi-quantitative Colorimetry

pH, Fecal 0020518
Method: Quantitative pH Indicator Strips/Quantitative pH Meter

Celiac Disease Reflexive Cascade 2008114
Method: Quantitative Nephelometry/Semi-Quantitative Enzyme-Linked Immunosorbent Assay//Semi-Quantitative Indirect Fluorescent Antibody

Fat, Fecal Qualitative 0020385
Method: Qualitative Microscopy/Stain


Results cannot be used if patient on low-fat diet

Fat, Fecal Quantitative, Homogenized Aliquot 2002350
Method: Nuclear Magnetic Resonance Spectroscopy


Results cannot be used if patient on low-fat diet

Fat, Fecal Quantitative 24-Hour Collection (Includes Homogenization) 2002354
Method: Nuclear Magnetic Resonance Spectroscopy

Fat, Fecal Quantitative 48-Hour Collection (Includes Homogenization) 2002355
Method: Nuclear Magnetic Resonance Spectroscopy

Fat, Fecal Quantitative 72-Hour Collection (Includes Homogenization) 2002356
Method: Nuclear Magnetic Resonance Spectroscopy

Pancreatic Elastase, Fecal by ELISA 0080526
Method: Quantitative Enzyme-Linked Immunosorbent Assay


If pancreatic insufficiency is present, consider cystic fibrosis testing


Choosing Wisely. An initiative of the ABIM Foundation. [Accessed: Nov 2017]

Holbrook I, British society of Gastroenterology. The British Society of Gastroenterology guidelines for the investigation of chronic diarrhoea, 2nd edition. Ann Clin Biochem. 2005; 42(Pt 3): 170-4. PubMed

General References

Abenavoli L, Proietti I, Vonghia L, Leggio L, Ferrulli A, Capizzi R, Mirijello A, Cardone S, Malandrino N, Leso V, Rotoli M, Amerio PL, Gasbarrini G, Addolorato G. Intestinal malabsorption and skin diseases. Dig Dis. 2008; 26(2): 167-74. PubMed

Ammoury RF, Croffie JM. Malabsorptive disorders of childhood. Pediatr Rev. 2010; 31(10): 407-15; quiz 415-6. PubMed

Chapman TP, Chen LY, Leaver L. Investigating young adults with chronic diarrhoea in primary care. BMJ. 2015; 350: h573. PubMed

Holt PR. Intestinal malabsorption in the elderly. Dig Dis. 2007; 25(2): 144-50. PubMed

Juckett G, Trivedi R. Evaluation of chronic diarrhea. Am Fam Physician. 2011; 84(10): 1119-26. PubMed

Montalto M, Santoro L, D'Onofrio F, Curigliano V, Visca D, Gallo A, Cammarota G, Gasbarrini A, Gasbarrini G. Classification of malabsorption syndromes. Dig Dis. 2008; 26(2): 104-11. PubMed

Schiller LR. Diarrhea and malabsorption in the elderly. Gastroenterol Clin North Am. 2009; 38(3): 481-502. PubMed

Schiller LR. Management of diarrhea in clinical practice: strategies for primary care physicians. Rev Gastroenterol Disord. 2007; 7 Suppl 3: S27-38. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Beal SG, Couturier MR, Gander RM, Doern CD. Diagnostic Algorithm for the Diagnosis of Pediatric Parasitic Gastroenteritis. J Clin Lab Anal. 2016; 30(2): 155-60. PubMed

Erickson A, Aldeen WE, Grenache DG, Ashwood ER. Evaluation of a fecal pancreatic elastase-1 enzyme-linked immunosorbent assay: Assessment versus an established assay and implication in classifying pancreatic function. Clin Chim Acta. 2008; 397(1-2): 87-91. PubMed

Hackenmueller SA, Grenache DG. Reference Intervals for Intestinal Disaccharidase Activities Determined from a Non-Reference Population. American Association for Clinical Chemistry. [Published: Sep 2016; Accessed: Nov 2017]

Lu J, Pulsipher BS, Grenache DG. An automated method for the measurement of total protein in homogenates of intestinal mucosa. Clin Chim Acta. 2013; 421: 59. PubMed

Medical Reviewers

Content Reviewed: 
March 2017

Last Update: October 2017