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 MSt MRCGP.

Posted: 16 August 2025Updated: 16 August 2025 Guideline-Aligned (High Confidence) Clinically Reviewed

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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What Role Do Stool Tests Play: Guideline-aligned Answer | iatroX