What role do stool tests play in the investigation of chronic diarrhoea, and which specific tests should I order?

Guideline-aligned answer with reasoning, red flags and references. Clinically reviewed by Dr Kola Tytler MBBS CertHE MBA MRCGP.

Posted: 16 August 2025Updated: 16 August 2025 Guideline-Aligned (High Confidence) Clinically Reviewed
Dr Kola Tytler MBBS CertHE MBA MRCGPClinical Lead • iatroX

Stool tests are important in the investigation of chronic diarrhoea, especially when an infectious cause is suspected or to help differentiate between inflammatory and functional bowel conditions .

Specific stool tests that should be ordered, depending on the clinical context, include:

  • Routine microbiology investigation and examination for ova, cysts, and parasites: This is considered if an infectious cause is suspected or if there is a history of exotic foreign travel . Three specimens should be sent at least two days apart, as ova, cysts, and parasites are shed intermittently .
  • Clostridioides difficile testing: This test is particularly relevant if the person has recently been admitted to hospital, treated with antibiotics or a proton pump inhibitor, or if a previous episode of diarrhoea has resolved and symptoms have recurred .
  • Faecal calprotectin testing: This test helps to differentiate between irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) . It is typically considered for people under the age of 40 years if specialist assessment is being considered and cancer is not suspected . Faecal calprotectin should not be used for individuals with new onset rectal bleeding or bloody diarrhoea, or when there is a need to rule out cancer .

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