Chronic Diarrhoea in General Practice: A Structured Approach to Diagnosis and Stool Testing
A practical guide for Australian GPs on assessing chronic diarrhoea, including key history, red flags, coeliac screening, and appropriate stool investigations such as faecal calprotectin, stool MCS, H. pylori antigen, occult blood, and faecal elastase.
Chronic Diarrhoea in General Practice: A Structured Approach to Diagnosis and Stool Testing
Chronic diarrhoea is a common presentation in general practice.
But it is not a diagnosis.
It is a symptom.
It is generally defined as:
Loose or watery stools lasting longer than four weeks.
The clinical challenge is not ordering every test.
The challenge is understanding which test answers which clinical question.
A structured approach helps avoid unnecessary investigations while identifying serious pathology early.
Table of Contents
- Step 1: Clarify the Symptom Properly
- Step 2: Identify Red Flags
- Step 3: Initial Blood Tests
- Coeliac Serology
- Why Coeliac Disease Matters
- Step 4: Stool Investigations — What to Order and Why
- Step 5: Differential Diagnosis of Chronic Diarrhoea
- Step 6: Management Overview
- When to Refer
- A Practical GP Workflow
- Final Thoughts
- Explore AI Tools for Structured Clinical Consultations
Step 1: Clarify the Symptom Properly
Before ordering investigations, the first step is to clarify the symptom in detail.
Important questions include:
- How many bowel motions per day?
- Are there nocturnal symptoms?
- Is there blood or mucus?
- Any unintentional weight loss?
- Bloating or excessive gas?
- Abdominal pain?
- Steatorrhoea (floating or oily stools)?
- Recent travel history?
- Recent antibiotic use?
- Food triggers?
- Relation to stress or anxiety?
This helps distinguish between several important patterns:
| Pattern | Possible Cause |
|---|---|
| True diarrhoea | infection, inflammatory disease |
| IBS-type loose stools | functional bowel disorder |
| Malabsorption | coeliac disease, pancreatic insufficiency |
| Inflammatory diarrhoea | IBD, microscopic colitis |
| Overflow diarrhoea | severe constipation |
Good history-taking often narrows the differential before any tests are ordered.
Step 2: Identify Red Flags
Certain features suggest organic pathology and should prompt early investigation or referral.
Red flags include:
- unintentional weight loss
- iron deficiency anaemia
- rectal bleeding
- family history of colorectal cancer
- new onset diarrhoea after age 50
- persistent nocturnal diarrhoea
- raised inflammatory markers
These patients often require colonoscopy or specialist referral.
For colorectal cancer screening guidance see:
Australian Government National Bowel Cancer Screening Program
Step 3: Initial Blood Tests
Baseline investigations often include:
- full blood examination (FBE)
- CRP or ESR
- electrolytes and renal function
- liver function tests
- thyroid function (TSH)
- iron studies
- vitamin B12
- folate
These tests help screen for:
- inflammatory disease
- malabsorption
- endocrine causes
- nutritional deficiency
Coeliac Serology
Always consider coeliac disease when assessing chronic diarrhoea.
Recommended tests include:
- tissue transglutaminase IgA (tTG-IgA)
- total IgA level
If the patient is IgA deficient:
- order deamidated gliadin peptide (DGP) IgG
Important clinical point:
Patients must be consuming gluten at the time of testing.
Starting a gluten-free diet before testing may produce false negative results.
For national guidance see:
Coeliac Australia – Testing for Coeliac Disease
Why Coeliac Disease Matters
Coeliac disease can present with:
- chronic diarrhoea
- bloating
- iron deficiency
- fatigue
- weight loss
- osteopaenia
- infertility
- neurological symptoms
Some patients have minimal gastrointestinal symptoms, making diagnosis easy to miss.
Consider screening in patients with:
- unexplained iron deficiency
- autoimmune thyroid disease
- type 1 diabetes
- persistent fatigue
Positive serology usually leads to confirmatory endoscopic biopsy.
Step 4: Stool Investigations — What to Order and Why
Stool testing should be targeted, not routine.
Each test answers a specific clinical question.
Stool MCS (Microscopy, Culture and Sensitivity)
Consider when:
- infectious diarrhoea suspected
- travel history present
- recent antibiotic use
- immunocompromised patient
- acute-on-chronic symptoms
Detects:
- bacterial pathogens
- ova and parasites
- C. difficile (when requested)
Avoid routine ordering in clear IBS without red flags.
Faecal Calprotectin
Faecal calprotectin is useful for distinguishing:
| Condition | Typical Result |
|---|---|
| Irritable bowel syndrome (IBS) | normal |
| Inflammatory bowel disease (IBD) | elevated |
Elevated levels may suggest:
- Crohn's disease
- ulcerative colitis
- significant intestinal inflammation
Normal calprotectin strongly supports a functional disorder.
This test is particularly helpful in younger patients with chronic diarrhoea.
Stool Occult Blood (iFOBT)
Indicated when there is concern for colorectal pathology.
Examples include:
- unexplained anaemia
- subtle bleeding symptoms
- colorectal cancer screening
A positive result typically leads to colonoscopy referral.
Faecal Elastase
Faecal elastase helps identify pancreatic exocrine insufficiency.
Clinical clues include:
- steatorrhoea
- weight loss
- fat-soluble vitamin deficiency
- chronic alcohol use
- previous pancreatitis
Low faecal elastase suggests pancreatic insufficiency.
Stool Antigen Test for H. pylori
Important clarification:
H. pylori does not typically cause chronic diarrhoea.
It is primarily associated with:
- gastritis
- peptic ulcer disease
- dyspepsia
Testing is appropriate when patients present with:
- upper gastrointestinal symptoms
- unexplained iron deficiency
- family history of gastric cancer
Avoid reflex testing in isolated diarrhoea.
Step 5: Differential Diagnosis of Chronic Diarrhoea
Chronic diarrhoea can arise from several categories.
Functional
- IBS-D
- post-infectious IBS
Inflammatory
- Crohn's disease
- ulcerative colitis
- microscopic colitis
Malabsorption
- coeliac disease
- pancreatic insufficiency
- bile acid diarrhoea
- lactose intolerance
Endocrine
- hyperthyroidism
Medication-Induced
Common culprits include:
- metformin
- SSRIs
- magnesium supplements
- laxatives
- antibiotics
Lifestyle Contributors
Lifestyle factors may also contribute:
- alcohol excess
- artificial sweeteners
- excessive caffeine
- cannabis use
Always review medication lists and lifestyle factors before escalating investigations.
Step 6: Management Overview
Management depends on the underlying cause.
Coeliac Disease
Management includes:
- lifelong gluten-free diet
- dietitian referral
- bone density assessment
- monitoring iron, B12 and vitamin D
- monitoring tTG antibodies
Early diagnosis helps prevent complications.
IBS-D
Management options include:
- low FODMAP diet
- stress management
- gut-directed therapies
- psychological interventions
Inflammatory Bowel Disease
Requires:
- gastroenterology referral
- anti-inflammatory therapy
- monitoring inflammatory markers
Pancreatic Insufficiency
Treatment includes:
- pancreatic enzyme replacement therapy
- nutritional support
When to Refer
Referral is appropriate when:
- red flag symptoms are present
- coeliac serology is positive
- faecal calprotectin is elevated
- persistent symptoms remain despite negative investigations
- significant weight loss occurs
- diagnostic uncertainty remains
A Practical GP Workflow
For chronic diarrhoea lasting longer than four weeks:
- Detailed clinical history
- Screen for red flags
- Blood tests including coeliac serology
- Targeted stool testing
- Specialist referral if indicated
Targeted stool testing may include:
- stool MCS (infection suspected)
- faecal calprotectin (IBD vs IBS)
- occult blood (cancer risk)
- faecal elastase (malabsorption)
Avoid blanket testing.
Investigations should answer specific clinical questions.
Final Thoughts
Chronic diarrhoea is common in general practice — but its causes are diverse.
Effective assessment depends on:
- careful history-taking
- recognition of red flags
- coeliac screening
- targeted stool testing
- structured differential diagnosis
- appropriate follow-up
When approached systematically, most cases can be diagnosed and managed effectively within primary care.
Explore AI Tools for Structured Clinical Consultations
If you want to structure complex consultations more efficiently in general practice:
- Explore the GPCCMP Generator
- Try the AI Agent for GPs
- Access mental health planning tools via the MHCP Generator
- View the full workflow suite on the Caredevo Offer Page
- Read more insights on the Caredevo Blog
Next step
See how AI can help you structure complex gastroenterology consultations in general practice.