Diarrhoea & stool changes

Pre-referral guidelines for primary care providers

This guideline will cover

  • chronic diarrhoea (> 2 weeks)
  • Toddler's diarrhoea
  • lactose intolerance
  • bloody stool
  • mucousy stools

It is important to remember that loose stools are very common in normal children at many ages, particularly in infancy and toddlers.

Infant stool patterns are often described as being normal when a bowel action occurs at a frequency of seven times per day through to once every seven days (or three times per day to once every three days in formula fed babies). They are often of variable consistency. Colour changes are common and generally do not represent an underlying abnormality. Straining in babies before passing a normal stool also does not represent an underlying problem.

For the management of gastroenteritis with acute diarrhoea (up to 2 weeks in duration) +/- vomiting, please refer to the Royal Children’s Hospital clinical practice guidelines.

For the management of constipation please see the relevant pre-referral guideline.


Chronic diarrhoea (greater than 2 weeks) can be caused by many different conditions, and a thorough history and examination is essential before considering any investigations. It is often normal for perfectly healthy infants and Toddler's (see Toddler's diarrhoea below). Diagnoses to consider include:

Toddler's diarrhoea is a common entity seen in children up to 5 year of age. It is an benign self-limiting phenomenon characterised by >3 loose stool per day, often with undigested food. High fluid intake, high dietary sugars including fructose (fruit or fruit juice), a low fat diet and an immature digestive tract all contribute to Toddler’s diarrhoea, which remains a benign condition.

Lactose intolerance is commonly misunderstood, and is primary (exceedingly rare), secondary or acquired. It is diagnosed on history of frothy stools and is rarely a diagnosis in its own right, rather indicating an underlying pathology. Testing of stool for reducing substances is generally not required in most cases.

  • primary lactose intolerance occurs in 1 in 1,000,000 children, with severe intolerance from birth (including to breast milk), an unwell child and associated developmental difficulties. There is no racial predilection.
  • secondary lactose intolerance is common and transient, usually due to either cow's milk protein enteropathy or infections (primarily rotavirus). There is no racial predilection.
  • acquired lactose intolerance is more common in Asian and African families and is characterised by a gradual reduction in lactase production, resulting in bowel symptoms with dairy intake in the adolescent to adult age, almost never seen in younger children.

Bloody stool (haematochezia) is a sign of damage to the gut mucosa and may be acute or chronic. It is important to distinguish between:

  • blood on the stool (more likely a distal cause): causes to consider include anal tear or fissure, haemorrhoid
  • blood mixed through the stool: causes to consider include swallowed maternal blood (newborns), infections, cow's milk protein intolerance, inflammatory bowel disease (generally requires > 6 weeks of symptoms) or, rarely, Meckel's diverticulum.

Mucousy stool is a sign of mucosal inflammation, with very similar causes as that of bloody stool. Persistent mucous in the stool may also raise concern for malabsorption.

Constipation - please see constipation pre-referral guideline.

Practice points

  • Diarrhoea is defined as chronic when present for more than 2 weeks
  • Loose stools are very common in normal children at many ages, particularly in infancy and toddlers.
  • Infant stools can occur seven every day to once every seven days (or three every day to one every three days in formula fed babies).
  • Lactose intolerance is commonly misunderstood. It can be primary (exceedingly rare), secondary or acquired - thus symptomatic improvement with removal of lactose from the diet should not preclude further consideration of the underlying cause.


Chronic diarrhoea (> 2 weeks) is common in infants and toddlers, thus in well children under 5 years of age with a typical history, normal examination and no red flags, further investigation is not required.

  • Investigations could include:
    • First line: stool M/C/S & O/C/P, stool multiplex PCR, stool C. diff toxin, FBE, ESR, UEC
    • Second line (referral to paediatric outpatient services to be considered first): sweat test, faecal fat crystals and globules, stool electrolytes (and osmolality), hydrogen breath test
    • Further investigations are guided by findings and clinical presentation.
  • Management is directed at any positive findings. Keep in mind that many stool organisms found on routine stool culture in children are non-pathogenic organisms that rarely cause symptoms and do not require treatment in immune competent children (e.g. Blastocystis hominis, Dientamoeba fragilis).

Toddler's diarrhoea requires no investigation or further management.

Lactose intolerance can usually be diagnosed clinically, although stool reducing substances can be undertaken when unsure. This is generally a secondary diagnosis (see above), thus symptomatic improvement with removal of lactose from the diet should not preclude further consideration of the underlying cause.

Bloody stool can generally be diagnosed with a good history and examination, although further testing may be warranted, including:

  • faecal occult blood (confirming true presence of blood if in doubt)
  • FBE, CRP, ESR, stool M/C/S

Mucousy stool can be approached in a similar fashion to bloody stool.

Referral pathways