Stool Testing: What It Can and Cannot Tell You
Level 3, Clinical application
In brief
Several stool tests are well validated and clinically valuable: faecal immunochemical testing for blood, faecal calprotectin for intestinal inflammation, faecal elastase for pancreatic insufficiency, Helicobacter pylori stool antigen, Clostridioides difficile testing and pathogen and parasite testing. Comprehensive commercial stool profiles add microbiome composition and markers such as secretory IgA, zonulin and beta glucuronidase, which have limited clinical validation. Choosing the right test for a defined question matters most.
Stool is an underused and overused clinical sample. Underused, because several simple, validated stool tests could identify important conditions earlier and are sometimes forgotten. Overused, because comprehensive commercial stool profiles, reporting dozens of markers and microbial species, are often ordered without a clear question and interpreted with more confidence than the evidence allows. This article sets out what stool tests can and cannot tell practitioners.
Validated tests and their uses
| Test | Main use | Practical points |
|---|---|---|
| Faecal immunochemical test (FIT) | Detects human blood; used in bowel cancer screening and to triage people with bowel symptoms | In some health systems, FIT results guide urgency of referral in symptomatic patients; a negative result does not exclude all serious disease when red flags are present |
| Faecal calprotectin | Marker of intestinal inflammation; helps distinguish inflammatory bowel disease from irritable bowel syndrome in younger adults | Raised by NSAIDs, proton pump inhibitors, gastrointestinal infection and some other conditions; results in a grey zone may be repeated |
| Faecal lactoferrin | Alternative marker of intestinal inflammation | Similar uses to calprotectin |
| Faecal elastase | Assesses exocrine pancreatic function | Watery stool can falsely lower results; low values suggest pancreatic insufficiency |
| Helicobacter pylori stool antigen | Diagnosis and confirmation of eradication | Proton pump inhibitors and recent antibiotics can cause false negatives; guidelines advise stopping them for a period before testing |
| Clostridioides difficile testing | Diagnosis of C. difficile infection in people with diarrhoea | Testing formed stool is not recommended, as colonisation without infection is common |
| Pathogen testing | Bacterial, viral and parasitic causes of diarrhoea | Multiplex PCR panels are sensitive and may detect organisms that are present but not causing illness |
| Ova, cysts and parasites | Parasitic infection, particularly after travel or in endemic regions | Multiple samples may be needed; serology is better for some parasites such as Strongyloides |
What comprehensive stool profiles add
Commercial comprehensive stool profiles typically combine some validated markers with a range of additional measures.
| Marker | Claimed meaning | Evidence status |
|---|---|---|
| Microbiome composition by sequencing or culture | Dysbiosis, beneficial and harmful bacteria | Healthy microbiomes vary widely; no validated reference for individuals; composition changes day to day; limited evidence that results guide effective treatment |
| Secretory IgA | Gut immune function | Levels vary; clinical significance for individual decisions not established |
| Zonulin | Intestinal permeability | A commonly used assay has been shown not to measure zonulin itself; not validated |
| Beta glucuronidase | Deconjugation of hormones and toxins | Biologically plausible; clinical meaning of individual results not established |
| Short chain fatty acids | Fermentation activity | Faecal levels reflect production and absorption; limited clinical use |
| Yeast and fungal culture | Fungal overgrowth | Candida is commonly present in healthy people; presence alone is not a diagnosis |
| Digestive markers such as fat and fibre | Digestion and absorption | Some value, but specific tests are more reliable |
These markers may be of research interest, and some practitioners find them useful for patient engagement, but they should not drive extensive treatment protocols on their own.
Common pitfalls
- Treating colonisation as infection. Sensitive PCR panels and cultures often detect organisms that are not causing symptoms.
- Ignoring medicines. NSAIDs raise calprotectin; proton pump inhibitors affect Helicobacter testing and calprotectin.
- Over interpreting microbiome reports. Labels such as low diversity or dysbiosis are not diagnoses.
- Missing red flags. Bleeding, weight loss, anaemia and new symptoms in older adults need medical investigation, including colonoscopy where indicated, regardless of stool profile results.
- Using stool tests for the wrong question. Coeliac disease is diagnosed by blood serology and biopsy; bile acid diarrhoea by specific tests; SIBO by breath testing or aspirate.
Choosing the right test
| Clinical question | Appropriate test |
|---|---|
| Is there inflammation in the bowel? | Faecal calprotectin, with blood tests |
| Is there blood in the stool? | FIT, alongside clinical assessment |
| Is the pancreas producing enough enzymes? | Faecal elastase |
| Is Helicobacter pylori present? | Stool antigen or urea breath test |
| Is acute diarrhoea caused by an infection? | Pathogen testing, C. difficile testing when indicated |
| Is there a parasite after travel? | Ova, cysts and parasites; serology for some parasites |
| What is the patient’s microbiome like? | Research interest; rarely changes management |
Worked cases
The younger adult with diarrhoea
A 24 year old man has had loose stools and abdominal pain for 3 months. His calprotectin is markedly raised on 2 occasions and he does not take NSAIDs. He is referred for colonoscopy, which confirms Crohn disease. A comprehensive stool profile ordered previously had reported dysbiosis and recommended probiotics; the validated marker within it had been overlooked.
The traveller
A 35 year old woman returns from travel with persistent diarrhoea and bloating. Pathogen testing identifies Giardia, which is treated. Her symptoms improve, although some bloating persists for several weeks, consistent with post infection changes.
The false negative
A 50 year old man with dyspepsia has a negative Helicobacter stool antigen test while taking a daily proton pump inhibitor. After stopping the medicine for the recommended period, the test is repeated and is positive. He receives eradication therapy.
The anxious patient with a microbiome report
A 40 year old woman with mild bloating has a comprehensive stool profile reporting low diversity and yeast overgrowth. Her calprotectin and elastase are normal. The practitioner explains the limits of the microbiome findings, notes that Candida is commonly present in healthy people, and focuses on dietary diversity and her irritable bowel syndrome symptoms rather than antifungal protocols.
The right question first
Stool tests are most useful when they answer specific, clinically important questions. A small number of validated tests do this well. Broader profiles may interest patients and researchers but rarely change management, and their validated components should never be lost among the rest.
Stool test questions
Which stool tests are most useful?
What can raise faecal calprotectin?
Are comprehensive stool microbiome profiles useful?
References and guidelines
- National Institute for Health and Care Excellence. Quantitative faecal immunochemical testing to guide colorectal cancer pathway referral in primary care (DG56). London: NICE; 2023.
- National Institute for Health and Care Excellence. Faecal calprotectin diagnostic tests for inflammatory diseases of the bowel (DG11). London: NICE; 2013.
- Malfertheiner P, Megraud F, Rokkas T, et al. Management of Helicobacter pylori infection: the Maastricht VI/Florence consensus report. Gut. 2022;71(9).
- McDonald LC, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by IDSA and SHEA. Clinical Infectious Diseases. 2018;66(7).
- Scheffler L, Crane A, Heyne H, et al. Widely used commercial ELISA does not detect precursor of haptoglobin2, but recognizes properdin as a potential second member of the zonulin family. Frontiers in Endocrinology. 2018;9:22.
Continue your learning
Ordering stool tests with purpose
Stool testing is covered in the Gut Dysfunction module of IIFM’s 6 month Functional Medicine and Clinical Nutrition program, where practitioners learn which tests answer which questions.
This article is for the education of healthcare professionals. It is not a substitute for individual medical advice, diagnosis or treatment, and does not change any practitioner’s scope of practice. Regulation and guidelines differ between countries.