Paediatrics chapters

Chronic diarrhoea and malabsorption

Diarrhoea lasting more than two weeks: persistent infective diarrhoea versus chronic non-infective causes, osmotic versus secretory diarrhoea, malabsorption, key stool tests and treatment by cause.

UHS PGET syllabus: Gastrointestinal and liver disorders (12 MCQs), Chronic diarrhoea: definition; causes/aetiologies and pathogens; dehydration assessment; managementUpdated November 2026
In 30 seconds
  • Diarrhoea lasting more than 14 days is persistent if it began as an infective episode, and chronic when the cause is usually non-infective; it leads to malabsorption and malnutrition.
  • Osmotic diarrhoea stops with fasting (lactose intolerance, sorbitol, laxatives; stool osmotic gap above 50), while secretory diarrhoea continues during fasting (gap below 50).
  • Main causes: post-infective lactose intolerance, cow's milk protein allergy, giardiasis, coeliac disease, cystic fibrosis, toddler's diarrhoea, IBD; treat the cause, keep feeding and correct deficiencies.
On this page

Overview

Diarrhoea that goes on for more than two weeks is a different problem from acute gastroenteritis. In our setting the commonest form is persistent diarrhoea: an infective episode that fails to settle, usually in a malnourished child, which carries a much higher death rate than acute diarrhoea. Elsewhere, chronic diarrhoea is mostly non-infective: sugar intolerance, milk allergy, coeliac disease, cystic fibrosis, toddler's diarrhoea and IBD. The aim is to find the mechanism, correct dehydration and nutrition, and treat the cause.

Definitions

TermMeaning
Diarrhoea (physiological)Stool output above 15 g/kg/day in infants or 200 g/day in older children (Akbar); Nelson uses over 10 mL/kg/day
Persistent diarrhoeaAn episode that starts acutely, is thought to be infective, and lasts more than 14 days
Chronic diarrhoeaDiarrhoea lasting more than 2 weeks, usually of non-infective cause
MalabsorptionFailure to digest or absorb nutrients, the usual end result when diarrhoea persists
High-yield

About 5 to 15% of acute episodes become persistent, but the case fatality is 5 to 7% (versus about 1% for acute diarrhoea), and 30 to 50% of all diarrhoeal deaths are from persistent diarrhoea (Akbar).

Mechanisms

FeatureOsmotic diarrhoeaSecretory diarrhoea
Basic defectUnabsorbed solute pulls water into the lumen (maldigestion, transport defect, non-absorbable substance)Active chloride secretion by the gut, reduced absorption
When fastingStopsContinues
StoolWatery, acidic, reducing substances presentWatery, large volume, normal osmolality
Osmotic gapWell above 50 (Akbar uses above 100)Below 50 (Akbar uses below 100)
Stool white cellsNoneNone
ExamplesLactose intolerance, sorbitol/fruit juice, laxatives (PEG, milk of magnesia)Cholera, ETEC, neuroendocrine (VIP) tumours, congenital chloride diarrhoea

Other mechanisms: reduced absorptive surface (short bowel, mucosal disease such as coeliac), fast transit (irritable bowel, thyrotoxicosis), and mucosal inflammation (IBD, invasive infection: blood and pus cells in stool).

Worked example: stool osmotic gap

Osmotic gap = 290 − 2 × (stool Na + stool K)
Stool Na 30, K 30: 290 − 2 × 60 = 170 → osmotic
Stool Na 70, K 60: 290 − 2 × 130 = 30 → secretory

Exam trap

Most real diarrhoeas are mixed. A child with viral enteritis may slow down while nil by mouth but not stop completely, because inflammation adds a secretory component.

Causes

Persistent diarrhoea (infective start)

GroupCauses
BacteriaE. coli, Shigella, non-typhoid Salmonella, Campylobacter
ProtozoaGiardia lamblia, Entamoeba histolytica, Cryptosporidium
Host factorsRepeated episodes, badly managed acute episode, malnutrition, secondary lactose intolerance

Chronic diarrhoea by age (Nelson)

AgeCommon causes
InfantPost-infective secondary lactase deficiency, cow's milk/soy protein intolerance, toddler's diarrhoea, coeliac disease, cystic fibrosis, AIDS enteropathy
ChildPost-infective lactase deficiency, irritable bowel syndrome, coeliac disease, lactose intolerance, giardiasis, IBD
AdolescentIrritable bowel syndrome, IBD, lactose intolerance, giardiasis, laxative misuse, coeliac disease

Rare causes: congenital chloride diarrhoea, acrodermatitis enteropathica (zinc), intestinal lymphangiectasia, abetalipoproteinaemia, short bowel syndrome, autoimmune enteropathy, Hirschsprung enterocolitis, secretory tumours.

Important specific conditions

Secondary (post-infective) lactose intolerance

  • Lactase sits on mature cells at the villus tip. After rotavirus or other enteritis, the tip cells are replaced by immature cells with little lactase.
  • Watery diarrhoea, bloating, flatulence, colicky pain, worse with milk.
  • Stool pH acidic and reducing substances positive; hydrogen breath test positive.
  • Treatment: reduce or remove lactose for a while (lactose-reduced formula, low-lactose milk); yoghurt is usually tolerated because its bacteria make lactase; hard cheese has little lactose. It recovers as the mucosa heals.
  • Congenital lactase deficiency is rare and causes symptoms from the first milk feeds.

Cow's milk protein allergy

  • Starts mostly in the first 3 months; more common in boys and with a family history of atopy; prevalence about 0.5 to 1%.
  • Colic, vomiting, diarrhoea; stools with flecks of blood and mucus; irritability.
  • Diagnosis is mostly clinical, by response to removing cow's milk protein.
  • Treatment: remove cow's milk and all its products (and from the mother's diet if breastfeeding). Substitute:
FormulaPoint
Soy formulaTolerated by about 50 to 80%; not suitable if also soy-allergic
Extensively hydrolysed formulaCow's milk proteins broken down by enzymes so they no longer trigger symptoms
Amino-acid formulaNeeded in about 10%; tolerated by almost all

Long-term exclusion needs an alternative source of calcium and protein.

Giardiasis

  • Commonest protozoal cause of chronic relapsing diarrhoea in children; spreads by ingesting cysts in water or by person-to-person contact; trophozoites live in the duodenum.
  • Greasy, foul-smelling stools without blood, bloating, flatulence, anorexia, abdominal pain, weight loss; may cause malabsorption, secondary lactose intolerance and vitamin A and iron deficiency.
  • Diagnosis: cysts or trophozoites in fresh stool (three samples improve yield) or Giardia antigen in stool (Nelson calls stool immunoassay the test of choice).
  • Treatment (Akbar): metronidazole is the drug of choice; alternatives tinidazole, nitazoxanide, albendazole, quinacrine.

Toddler's diarrhoea (chronic non-specific diarrhoea)

  • Usually 6 to 36 months of age; loose stools with visible food (peas, carrots) and mucus, often alternating with normal stools.
  • Growth and weight gain are normal; diarrhoea is rare during sleep.
  • Linked to excess fruit juice and sweet drinks (sorbitol and fructose overload).
  • Treatment: reassurance and cutting down juice; no drugs.
Memory hook

"Peas and carrots, growing well" = toddler's diarrhoea.

Other causes covered elsewhere

  • Coeliac disease: gluten enteropathy; anti-tTG IgA and duodenal biopsy.
  • Cystic fibrosis: pancreatic insufficiency with bulky, oily stools; sweat chloride over 60 mmol/L on two occasions.
  • IBD: bloody diarrhoea, weight loss, raised inflammatory markers.

Clinical features of malabsorption

  • Early: frequent, bulky, pale, oily (steatorrhoeic) stools, weight loss, often good appetite.
  • Late: failure to thrive, muscle wasting, protuberant abdomen, repeated infections.
  • Specific deficiencies: iron and folate (anaemia), vitamin B12 (anaemia), vitamin D and calcium (rickets, hypocalcaemic tetany), vitamin K (bleeding).
  • The malnutrition-diarrhoea cycle: malnutrition lowers bile acids, pancreatic enzymes and disaccharidases and alters flora, which prolongs diarrhoea, which worsens malnutrition.

Investigations

TestWhat it shows
CBC, ESR/CRPAnaemia, inflammation (IBD)
Serum electrolytes, albuminDehydration, protein loss
Stool microscopy (three fresh samples)Ova, cysts, trophozoites, pus cells, blood, eosinophils
Stool cultureBacterial infection
Stool pH and reducing substancesSugar malabsorption (acidic, positive)
Hydrogen breath testLactose malabsorption (false negative on antibiotics)
Sudan stain / 72-hour faecal fatFat malabsorption: over 7% of dietary fat in stool
Faecal elastasePancreatic insufficiency
D-xylose testMucosal carbohydrate absorption
Coeliac serology (with total IgA)Coeliac disease
Sweat chlorideCystic fibrosis
Endoscopy and small bowel biopsyCoeliac disease, giardiasis, lymphangiectasia, IBD
C. difficile toxinDiarrhoea after antibiotics

Management

General

  • Assess and correct dehydration with the same signs and Plans as acute diarrhoea; use ORS where possible, IV fluids if needed.
  • Continue feeding: keep breastfeeding; give small frequent energy-dense meals (for example yoghurt, khichri); reduce lactose if intolerance is suspected.
  • Micronutrients: vitamin A, zinc, folate, iron and other vitamins (Akbar).
  • Antibiotics only for a specific infection (Shigella dysentery, Giardia, amoebiasis).
  • Severe persistent diarrhoea with dehydration (IMNCI) needs referral to hospital.

By cause

CauseTreatment
Post-infective enteropathyElemental or hydrolysed formula until mucosa heals
Lactose intoleranceLactose exclusion or reduction
Cow's milk protein allergyRemove cow's milk protein; hydrolysed or amino-acid formula
GiardiasisMetronidazole
Coeliac diseaseLifelong gluten-exclusion diet
Cystic fibrosisPancreatic enzymes with meals, high-energy diet, fat-soluble vitamins
Toddler's diarrhoeaReassurance, less juice
Irritable bowel syndromeHigh-fibre diet, behaviour measures
Hirschsprung enterocolitisFluids and antibiotics; definitive surgery
Exam trap

Do not stop feeding a child with persistent diarrhoea. Starvation worsens the mucosal damage and malnutrition.

Exam focus

Expect: the 14-day definition of persistent diarrhoea and its higher mortality; osmotic versus secretory diarrhoea (fasting test and osmotic gap); acidic stool with reducing substances in lactose intolerance; cow's milk allergy with blood-streaked stools in a young infant and the choice of substitute formula; Giardia as the commonest protozoal cause with greasy stools and metronidazole treatment; toddler's diarrhoea with normal growth and food particles; the tests for fat malabsorption; and the rule to continue feeding with micronutrient supplements.

Quick revision

  • Persistent: infective, over 14 days; chronic: over 2 weeks, mostly non-infective.
  • Osmotic stops with fasting, gap over 50; secretory continues, gap under 50.
  • Lactose intolerance: acidic stool, reducing substances, positive breath hydrogen.
  • Cow's milk allergy: under 3 months, blood and mucus, hydrolysed formula.
  • Giardia: greasy foul stools, duodenum, metronidazole.
  • Toddler's diarrhoea: food particles, normal growth, too much juice.
  • Malabsorption: steatorrhoea, wasting, rickets, anaemia, bleeding.
  • Keep feeding; add zinc, vitamin A, folate, iron.

Written by The House Job from standard references (Basis of Paediatrics by Pervez Akbar; Nelson Essentials of Paediatrics).

FAQ

What is the difference between persistent and chronic diarrhoea?

Persistent diarrhoea is an infective episode that started acutely and has lasted over 14 days; chronic diarrhoea lasts over 2 weeks and usually has a non-infective cause.

How can I tell osmotic diarrhoea at the bedside?

Keep the child nil by mouth on IV fluids: osmotic diarrhoea stops, secretory diarrhoea continues. The stool osmotic gap confirms it.

Can a child with lactose intolerance eat yoghurt?

Usually yes. Bacteria in yoghurt produce lactase, so it is well tolerated.

Does toddler's diarrhoea need treatment?

No drugs are needed. The child grows normally; reassurance and cutting down fruit juice and sweet drinks usually settle it.