A practical difference in New Zealand
Persistent watery diarrhoea may deserve assessment even when blood tests and stool tests such as FIT or calprotectin (a stool test for bowel inflammation) are normal. These tests cannot reliably exclude microscopic colitis. In New Zealand, the October 2026 Pharmac Schedule provides a Special Authority pathway for controlled-release budesonide capsules after colonoscopy and biopsy confirm collagenous or lymphocytic colitis.
Guidance behind this advice
Why a normal camera view can still need biopsies
Camera and tissue
A colon can look normal through the camera and still have microscopic colitis. The tissue sample is prepared and examined by a pathologist.
Camera and tissue
A colon can look normal through the camera and still have microscopic colitis. The tissue sample is prepared and examined by a pathologist.
Both sides of the colon
When microscopic colitis is suspected, biopsies from the right and left colon improve the assessment. The numbered points are examples of sampling sites, not a map of disease. Your right is on the left of this front-view picture.
Understanding the tissue words
Lymphocytic colitis has extra immune cells in the surface lining. Collagenous colitis has a thicker collagen layer just beneath it, and can also contain extra immune cells. These are related tissue patterns, not cancer stages. The drawings do not provide diagnostic cell counts or thickness.
Treatment and recurrence
Budesonide is commonly used for active microscopic colitis. If this condition is confirmed, I will discuss the treatment plan with you in clinic. If symptoms return, another course or individual maintenance treatment may be appropriate after review. This differs from the usual steroid advice for Crohn's and ulcerative colitis. I also check for another cause of ongoing diarrhoea.
Simplified illustrations, not to scale. These show an example, not your own anatomy or test result.
Read every diagram explanation
Camera and tissue
A colon can look normal through the camera and still have microscopic colitis. The tissue sample is prepared and examined by a pathologist.
Both sides of the colon
When microscopic colitis is suspected, biopsies from the right and left colon improve the assessment. The numbered points are examples of sampling sites, not a map of disease. Your right is on the left of this front-view picture.
Understanding the tissue words
Lymphocytic colitis has extra immune cells in the surface lining. Collagenous colitis has a thicker collagen layer just beneath it, and can also contain extra immune cells. These are related tissue patterns, not cancer stages. The drawings do not provide diagnostic cell counts or thickness.
Treatment and recurrence
Budesonide is commonly used for active microscopic colitis. If this condition is confirmed, I will discuss the treatment plan with you in clinic. If symptoms return, another course or individual maintenance treatment may be appropriate after review. This differs from the usual steroid advice for Crohn's and ulcerative colitis. I also check for another cause of ongoing diarrhoea.
What symptoms does it cause?
Watery poo, urgency and needing the toilet at night are typical. Some people have accidents, cramps, tiredness or weight loss. Symptoms can improve for a while and then return, affecting sleep, work and getting out of the house.
It is different from irritable bowel syndrome (IBS). Symptoms can overlap, but IBS does not produce the tissue changes of microscopic colitis. Visible bleeding is not typical and should be assessed rather than automatically attributed to this diagnosis.
Why take biopsies when everything looks normal?
During colonoscopy I inspect the lining and take small tissue samples. If I suspect microscopic colitis, I take samples from both the right and left sides of the colon. Even a normal-looking bowel needs biopsies to check for this condition. An earlier colonoscopy without these samples does not rule it out.
A pathologist examines the samples. Your report may describe collagenous colitis, with a thicker collagen layer beneath the surface cells, or lymphocytic colitis, with extra immune cells in the surface lining. Incomplete forms also occur. These are related microscopic patterns, not cancer stages.
What else can cause watery diarrhoea?
I review the symptom pattern, medicines, weight change and previous results. Blood and stool tests may check for infection, anaemia, dehydration or another cause of diarrhoea. Coeliac testing is recommended because the conditions can coexist. Keep eating gluten until coeliac assessment is complete unless your treating clinician advises otherwise.
A normal calprotectin result cannot reliably rule out microscopic colitis, and the test is not reliable for monitoring it. FIT checks for blood and cannot detect these microscopic changes. If treatment has not helped, I also consider other causes of diarrhoea, including bile acid diarrhoea.
Could a medicine be contributing?
Some medicines, including anti-inflammatory painkillers such as ibuprofen, acid-suppressing PPIs and certain antidepressants, have been associated with microscopic colitis. An association does not prove that a particular medicine caused your symptoms. These medicines can also cause diarrhoea through other mechanisms.
Bring a list of medicines, supplements and over-the-counter products, including recent changes. I review timing and why each medicine was started before suggesting a change. Do not stop prescribed medicines yourself.
How is microscopic colitis treated?
Oral budesonide is the usual first treatment when active microscopic colitis needs medication. If this condition is confirmed, I will discuss the treatment plan with you in clinic.
It is a steroid designed to act mainly in the bowel, although side effects and interactions remain possible. Follow the prescribed course and any reduction instructions rather than changing the dose yourself.
Symptoms can return after treatment finishes. A further course or a lower maintenance dose may be appropriate after review. This is different from the usual advice against steroid maintenance for Crohn's disease or ulcerative colitis.
If treatment continues, I consider bone health, other conditions and medicine interactions. Persistent symptoms need reassessment for other causes before increasing treatment.
What can help while treatment is being arranged?
Drink regularly. A pharmacist can advise about oral rehydration solution if diarrhoea is causing fluid loss, particularly if you have kidney or heart disease or a fluid restriction. Keep a short record of watery stools, night-time symptoms, weight and any suspected food triggers.
There is no proven diet that cures microscopic colitis. Reducing excess caffeine, alcohol or a clear individual trigger may help symptoms. Avoid broad food exclusions, particularly if losing weight. Loperamide or treatment for bile acid diarrhoea may help selected people, but agree this with your clinician rather than self-treating severe illness.
Do I need repeated colonoscopies?
Follow-up usually focuses on symptoms, nutrition and treatment safety. Repeat colonoscopy or biopsies are not routinely needed just to prove the microscopic changes have disappeared. New symptoms or another clinical question may still justify an examination.
Microscopic colitis has not been shown to increase colorectal cancer risk. It does not by itself require an IBD cancer-surveillance programme.
Routine bowel screening and follow-up for polyps, family history or other findings still apply. Your recommended endoscopy follow-up will be documented in your endoscopy and/or histology report once tissue results are available.
When to get help
Contact our team or your GP if diarrhoea returns, treatment is not helping, or you are losing weight. Seek urgent assessment for blood or black tarry poo, severe or worsening pain, fever with marked illness, repeated vomiting, or dehydration such as very little urine, dizziness or difficulty keeping fluids down. Do not assume these are simply microscopic colitis.
Call 111 if you collapse, are confused or too unwell to travel safely, or have heavy bleeding with faintness.
Three things to remember
- Microscopic colitis can be present when the colon looks normal. Biopsies establish the diagnosis.
- Normal calprotectin or a low FIT cannot reliably exclude microscopic colitis.
- Treatment and follow-up are individual. Recurring symptoms may need longer budesonide treatment or assessment for another cause.
Related information
Sources and further reading
English clinical master checked 16 October 2026.
- Medsafe: microscopic colitis and medicines, December 2022
- Pharmac: budesonide funding criteria, checked October 2026
- UEG and European Microscopic Colitis Group guideline, 2021
- ESGE: colon biopsy guidance, 2021
- AGA: medical management of microscopic colitis
- NIDDK: diagnosis and patient information
- NIDDK: symptoms and causes
- NIDDK: diet and nutrition
- Healthify: oral rehydration salts, reviewed July 2026