Malabsorption and nutrient deficiency

01OverviewDefinition, clinical context and the essential points that orientate the chapter.

Absorption depends on digestion, mucosal integrity, intestinal length, pancreatic enzymes, bile salts, lymphatic transport and adequate intake. Pancreatic insufficiency causes impaired fat and protein digestion; coeliac disease or Crohn's damages mucosa; ileal disease impairs B12 and bile-salt recovery; extensive resection reduces surface; small-bowel bacterial overgrowth alters nutrients; intestinal lymphangiectasia loses protein. A patient may have several mechanisms after surgery or with systemic disease.

History should describe stool frequency, nocturnal symptoms, oiliness and flushing, food relationship, abdominal surgery, pancreatitis, alcohol, travel, immune suppression, medicines, family history and autoimmune disease. Examination seeks weight and muscle loss, mouth or skin change, bruising, oedema, neuropathy, proximal weakness and bone tenderness. Blood counts and nutrients map consequences but rarely diagnose the mechanism alone.

Coeliac disease is a high-yield, treatable cause with a testable pathway. The person should consume gluten in more than one meal daily for at least six weeks before testing where possible. IgA tTG plus total IgA is usual first-line serology; specialist referral and duodenal biopsy remain important, although current 2026 BSG guidance may permit a no-biopsy diagnosis in carefully selected adults. That exception should be applied only through the live specialist pathway, not from a remembered antibody threshold.

Key points

Steatorrhoea, chronic diarrhoea, weight loss, bloating, anaemia, oedema, bruising, neuropathy or bone disease may be the presenting phenotype; absence of obvious stool fat does not exclude malabsorption.
Classify mechanisms: impaired intraluminal digestion, mucosal disease, reduced small-bowel surface, bile acid diarrhoea, lymphatic obstruction or mixed postoperative causes.
For coeliac testing, the patient must be eating gluten; check total IgA with IgA tissue transglutaminase and use appropriate IgG-based testing in IgA deficiency.
Do not advise a gluten-free diet before the diagnostic pathway is complete unless a specialist has agreed an alternative, because serology and histology can normalise.
Faecal elastase supports pancreatic exocrine insufficiency but watery diarrhoea can dilute the sample and cause a falsely low result.
Test for bile acid diarrhoea with SeHCAT or an accepted alternative where available rather than assuming every post-cholecystectomy or ileal symptom is IBS.
Replace iron, folate, B12, vitamin D, calcium and other deficits according to measured need, but check B12 before giving folic acid alone.
Severe depletion, tetany, arrhythmia, neurological deficit or high refeeding risk requires urgent correction and specialist nutrition support.

02AetiologyUnderlying causes, associations and risk factors, with why each one matters.

Impaired luminal digestion

Pancreatic exocrine insufficiency and inadequate bile delivery prevent normal breakdown and solubilisation of nutrients before epithelial absorption.

Small-intestinal mucosal disease

Coeliac disease, Crohn disease, infection and infiltrative disorders reduce surface area or disrupt transport across the intestinal lining.

Reduced surface or altered transport

Short bowel, postoperative anatomy, bile-acid loss, bacterial overgrowth and lymphatic obstruction impair absorption through distinct anatomical mechanisms.

03PathophysiologyThe causal sequence from the underlying abnormality to symptoms and harm.

1
Failed nutrient processing
Deficient enzymes or bile salts leave fat, protein and carbohydrate in forms that cannot be efficiently absorbed.
2
Epithelial or transport failure
Villous injury, reduced bowel length or lymphatic blockage prevents nutrients crossing into blood or lymph despite adequate intake.
3
Luminal loss and systemic depletion
Unabsorbed solutes draw water and undergo fermentation, while cumulative macro- and micronutrient deficits impair multiple organs.

04Clinical features and red flagsSymptoms, examination findings, patterns of presentation and time-critical warnings.

Fat malabsorption

Pale, bulky, difficult-to-flush or oily stool, weight loss and fat-soluble vitamin deficiency suggest pancreatic, biliary or small-bowel disease. Patients may use less specific terms, so ask concretely.

Coeliac phenotype

Chronic diarrhoea, bloating, iron-deficiency anaemia, aphthous ulcers, osteoporosis, dermatitis herpetiformis, autoimmune thyroid disease or a first-degree relative may prompt serology even without weight loss.

Pancreatic insufficiencyRed flag

Steatorrhoea, weight loss, diabetes, recurrent pancreatitis, pancreatic surgery or chronic epigastric pain suggests inadequate enzyme delivery; pancreatic cancer must be considered with new symptoms or jaundice.

Severe micronutrient complicationRed flag

Arrhythmia or tetany from electrolyte disturbance, confusion, ophthalmoplegia, profound anaemia, spinal-cord or peripheral nerve signs, or pathological fracture requires urgent correction and cause assessment.

Protein-losing or extensive disease

Oedema with low albumin, lymphopenia, major weight loss or broad deficiencies may indicate extensive mucosal disease, intestinal lymphatic loss, severe inflammation or liver or renal alternatives.

05InvestigationsWhat to request, why it matters and how to interpret it.

Investigation order

Read from the initial assessment onwards. Tests may run in parallel in urgent care; first-line, preferred, confirmatory, definitive and gold-standard labels appear only when the chapter explicitly states them.

01
Coeliac serology on a gluten-containing dietFirst step
Why
Measure total IgA and IgA tTG, with EMA for weakly positive results and IgG-based testing when IgA deficient according to the current pathway.
Interpretation and limitations
Positive serology warrants gastroenterology assessment; negative testing can be false after gluten restriction or in IgA deficiency. Persisting high suspicion may still require biopsy and HLA-informed specialist review.
02
Upper GI endoscopy with duodenal biopsies
Why
Obtain correctly oriented samples from the bulb and distal duodenum when the adult coeliac pathway or another mucosal diagnosis requires tissue.
Interpretation and limitations
Villous atrophy is not specific to coeliac disease. Histology must be interpreted with serology, gluten exposure, medicines, infection and immune disorders.
03
Faecal elastase
Why
Screen for moderate or severe pancreatic exocrine insufficiency using a formed stool sample where possible.
Interpretation and limitations
A low value supports insufficiency but watery diarrhoea can dilute it. A normal result is less reliable for mild disease; pancreatic imaging may still be needed.
04
Bile acid diarrhoea testing
Why
Use SeHCAT retention or a locally validated serum marker in persistent unexplained watery diarrhoea, particularly after ileal disease or cholecystectomy.
Interpretation and limitations
An abnormal result supports bile acid sequestrant therapy and provides severity information; empirical treatment alone can be confounded by poor tolerance or adherence.
05
Deficiency and inflammation profile
Why
Check FBC, ferritin and iron indices, B12, folate, calcium, phosphate, magnesium, vitamin D, albumin, INR, CRP, renal and liver profile, adding vitamins A, E, K, zinc or copper selectively.
Interpretation and limitations
Ferritin may be falsely normal in inflammation, macrocytosis can be absent with combined iron and B12 deficiency, and low albumin is nonspecific.
06
Small-bowel and pancreatic imaging
Why
Use MR enterography, CT, ultrasound, MRCP or EUS according to suspected Crohn's disease, tumour, chronic pancreatitis, obstruction or postoperative anatomy.
Interpretation and limitations
Imaging and endoscopy answer different questions. Capsule studies risk retention when stricture is plausible and do not assess pancreatic enzyme output.

06Differential diagnosisRealistic alternatives and the features that help distinguish them.

Coeliac disease

Positive serology while eating gluten and compatible duodenal histology identifies an immune enteropathy rather than nonspecific food intolerance.

Pancreatic exocrine insufficiency

Pancreatic disease, steatorrhoea, low faecal elastase and fat-soluble vitamin loss support maldigestion, with watery stool capable of falsely lowering elastase.

IBD, SIBO or bile-acid diarrhoea

Objective inflammation, altered anatomy, breath-test limitations and response to specialist testing help separate overlapping chronic-diarrhoea mechanisms.

07ManagementImmediate care, first-line treatment, alternatives and escalation.

01LocaliseFrom symptom to mechanismFirst stepChronic diarrhoea, steatorrhoea, weight loss or unexplained nutrient deficiency suggests impaired absorption.

1Confirm stool and weight phenotype, review diet, surgery, pancreas, ileum, medicines, travel and immune state, and assess dehydration or severe deficiency.
2Screen for coeliac disease while gluten is still consumed, inflammation and common deficiencies; add faecal elastase and bile acid testing according to phenotype.
3Use endoscopy and imaging to investigate mucosal disease, obstruction, pancreatic pathology or malignancy rather than labelling unexplained symptoms functional.
4Treat urgent depletion in parallel but retain baseline samples where safe so replacement does not erase diagnostic evidence.

02CoeliacComplete the coeliac pathwayCoeliac serology is positive or clinical suspicion remains high despite an equivocal result.

1Confirm adequate gluten exposure and total IgA, review antibody assay and refer to gastroenterology rather than starting diet treatment independently.
2Follow the current BSG adult algorithm for duodenal biopsy or a strictly selected no-biopsy pathway; label and orient specimens correctly.
3After diagnosis, provide expert dietetic education, assess baseline deficiencies and bone risk, and screen associated autoimmune conditions as indicated.
4Offer structured follow-up for symptoms, adherence, weight, serology and complications; investigate non-response rather than assuming deliberate gluten exposure.

03ReplaceCorrect deficiency safelyOne or more clinically important nutrient deficits are confirmed or strongly suspected.

1Treat immediately life-threatening electrolyte, thiamine, B12 or bleeding complications under the relevant emergency protocol.
2Select oral, intramuscular or intravenous replacement based on severity, symptoms, absorption, ongoing losses and cause; check interactions and renal function.
3Treat the mechanism with gluten exclusion only after diagnosis, pancreatic enzymes, bile acid therapy or inflammatory disease care as appropriate.
4Repeat clinical and biochemical assessment at a cause-specific interval and stop unnecessary long-term replacement only when stores and absorption are secure.

Key medicines and prescribing safety5 treatments · regimens, roles and cautions

Replaces pancreatic enzymes in confirmed exocrine insufficiency and improves digestion, stool consistency and nutrient uptake.

Pancreatin

Dose by lipase units with all meals and snacks, titrating to meal fat content, symptoms and weight under the current BNF and pancreatic specialist pathway; higher requirements may need acid suppression review.

Take during the meal rather than before or after it. Very high doses carry rare fibrosing-colonopathy risk; review persistent symptoms for adherence, timing, small-bowel disease or cancer.

Corrects megaloblastic anaemia and prevents or treats potentially irreversible neurological injury.

Vitamin B12 replacement

Use current BNF cause-specific oral or intramuscular hydroxocobalamin regimens; neurological involvement requires an urgent loading schedule and specialist follow-up.

Draw diagnostic samples first where safe, but never delay treatment for neurological disease. Potassium can fall during rapid marrow response, and the underlying cause determines lifelong need.

Restores haemoglobin and iron stores while the bleeding or malabsorptive cause is addressed.

Iron replacement

Choose an oral elemental-iron regimen or intravenous preparation according to severity, inflammation, absorption, blood loss and tolerance; follow current BNF and local infusion governance.

Oral preparations cause gastrointestinal effects and dark stool. Intravenous iron can cause infusion reactions and hypophosphataemia with some products; do not let replacement delay cancer investigation.

Corrects vitamin D deficiency and supports bone mineralisation in chronic malabsorption.

Colecalciferol with calcium when indicated

Use a current local loading and maintenance regimen based on vitamin D level, calcium intake, renal function and bone disease; avoid copying a single dose across patients.

Check adjusted calcium, renal disease, granulomatous disease and stone risk. Severe hypocalcaemia needs urgent monitored treatment, and magnesium deficiency may impede correction.

Binds excess colonic bile acids in confirmed bile acid diarrhoea.

Bile acid sequestrant

Use a locally titrated cholestyramine or alternative regimen after objective diagnosis where possible, separated from other medicines as the BNF specifies.

Constipation, bloating, poor adherence, medicine binding and long-term fat-soluble vitamin deficiency. Response or non-response alone is not a perfectly diagnostic test.

08ComplicationsImportant consequences, why they occur and why they matter clinically.

Anaemia, bone and neurological disease

Iron, folate, vitamin B12, calcium, vitamin D and other deficits cause cytopenias, fractures, neuropathy and cognitive or muscular symptoms.

Protein-energy malnutrition

Weight loss, sarcopenia and hypoalbuminaemic oedema reduce immunity, wound healing and treatment tolerance despite adequate appearing body mass.

Refeeding complications

Rapid nutrition after prolonged depletion can shift phosphate, potassium and magnesium intracellularly and precipitate cardiac, respiratory or neurological failure.

09Monitoring and follow-upTreatment response, safety checks and longer-term review.

Track stool frequency and character, weight, appetite and functional recovery using the same definitions at follow-up.
Repeat the specific depleted nutrient and relevant blood count after replacement, allowing enough time for the expected biological response.
Monitor calcium, phosphate, magnesium and renal function during intensive vitamin D or electrolyte correction.
For pancreatic enzymes, review timing with meals, dose adequacy, adherence, weight and fat-soluble vitamins; reassess the diagnosis if response is poor.
For coeliac disease, arrange dietetic review, symptom and weight assessment, serology and bone-health follow-up under current guidance.
Watch for refeeding shifts when severe malnutrition is corrected, even if malabsorption rather than low intake caused the depletion.
Ensure an urgent malignancy or inflammatory pathway remains active while symptomatic deficiencies improve.

10Special situationsVariants, exceptions and circumstances that change the usual approach.

A watery sample can mislead

Faecal elastase concentration falls with dilution. Repeat a low result on formed stool or interpret with imaging and pancreatic risk.

Iron can hide macrocytosis

Combined iron and B12 or folate deficiency may produce a normal MCV. Examine ferritin, transferrin saturation, B12, folate and the blood film together.

Serology needs gluten exposure

Antibody levels can fall quickly after dietary restriction. Explain why gluten should continue until the specialist diagnostic decision is complete.

The ileum has two signatures

Terminal ileal disease can cause B12 deficiency and bile acid diarrhoea; extensive disease can instead deplete the bile-salt pool and cause steatorrhoea.

Replacement response is evidence

Expected reticulocytosis, symptom change or nutrient recovery supports the treatment, while absent response should trigger adherence, ongoing loss, inflammation and diagnostic review.

11Common pitfallsFrequent interpretation and management errors.

01
Starting a gluten-free diet before coeliac serology and biopsy decisions are complete.
02
Diagnosing pancreatic insufficiency from one low faecal elastase in watery diarrhoea.
03
Giving folic acid alone before checking for B12 deficiency and neurological signs.
04
Replacing iron while failing to investigate gastrointestinal blood loss or cancer.
05
Calling chronic watery diarrhoea IBS without considering bile acid diarrhoea or microscopic colitis.
06
Assuming a normal MCV excludes combined nutrient deficiencies.