What exactly is microscopic colitis — and how many types are there?

Think of your colon as a tube lined with delicate tissue. In microscopic colitis, that lining is inflamed — but so subtly that when a doctor looks through the colonoscope, it appears normal. The trouble only shows up when tissue samples (biopsies) are examined under a microscope. ^[2]

There are two main subtypes, both producing very similar symptoms:

There are also "incomplete" or intermediate forms under active investigation, which carry a real risk of being missed if clinicians aren't specifically looking for them. ^[3] Global incidence sits around 8–12 cases per 100,000 person-years and has been rising steadily over recent decades. ^[4]

Causes: why does microscopic colitis happen?

There's no single cause. What we know is that it involves an abnormal immune response in the colon, triggered or sustained by several overlapping factors. In practice, the most relevant are:

1. Medications: the most avoidable trigger

If you're taking any of these and have had prolonged diarrhea, put it on the table in your next appointment. Sometimes withdrawing the suspect drug is all it takes. ^[5]

2. A misfiring immune system (autoimmune link)

Microscopic colitis frequently co-exists with other autoimmune conditions: coeliac disease, Hashimoto's thyroiditis, type 1 diabetes and rheumatoid arthritis. This isn't coincidence — it points to an underlying tendency for the immune system to attack the wrong targets in susceptible individuals. ^[6]

3. Gut infections and an altered microbiome

In some patients, the disease begins or flares after a bout of gastroenteritis. The role of the gut microbiome — the trillions of bacteria living in the colon — as a modulator of colonic inflammation is also under active investigation. ^[7]

Symptoms: what does microscopic colitis feel like?

The hallmark symptom is chronic watery diarrhea — and when I say watery, I mean it. Many patients report 5 to 10 completely liquid bowel movements a day. It's the kind of diarrhea that stops you living normally. ^[1]

The impact on quality of life can be enormous. Not being able to leave home without knowing where every bathroom is, turning down social plans, the shame of incontinence episodes — all of this matters and deserves to be taken seriously and treated properly. ^[8]

Risk factors: who is most likely to get it?

Microscopic colitis has a fairly well-defined patient profile: a woman over 60, often with other autoimmune conditions or taking one of the medications on the list above. But it does occur in men and in younger adults too — so it shouldn't be written off in other groups. ^[9]

Additional factors include alcohol consumption, obesity, gut microbiome alterations and a specific genetic background (HLA 8.1). And, as already noted, the list of potentially causative medications is long. ^[10]

If you have coeliac disease, autoimmune thyroiditis or rheumatoid arthritis and develop unexplained chronic diarrhea, microscopic colitis should be on the differential diagnosis list. This combination is more common than most people realise — and it is still regularly missed. ^[11]

Diagnosis: the colonoscopy trap

Here's where the classic pitfall lies. A patient has had diarrhea for months. A colonoscopy is ordered. The report comes back: "no significant findings." The patient is sent home without a diagnosis, thinking there's nothing wrong. But there is something wrong — the biopsies just weren't taken, or too few were collected.

The classic diagnostic triad is: chronic watery diarrhea + normal or near-normal colonoscopy + characteristic histological changes on biopsy. ^[12]

No blood or stool tests reliably diagnose microscopic colitis yet. Biomarkers are being researched, but histological examination of biopsies remains essential. ^[4]

What can it be confused with?

The differential diagnosis includes:

• • Irritable Bowel Syndrome (IBS) — easily confused, but IBS shows no biopsy changes in the colon.
• • Coeliac disease — can co-exist and should be actively ruled out.
• • Crohn's disease and ulcerative colitis — these do produce visible changes during colonoscopy.
• • Intestinal infections — always need to be excluded upfront.
• • Small intestinal bacterial overgrowth (SIBO).

If you've had persistent diarrhea without a clear diagnosis, I'd encourage you to explore our gastrointestinal disorders section or book a specialist consultation for a proper evaluation.

Treatment: there is a solution, and it works

The good news: microscopic colitis has effective treatment. The nuance: for some patients it's a chronic relapsing condition. But with the right approach, most people regain a normal quality of life. ^[13]

Step 1: Remove the offending drug (if there is one)

Always the first move. If a suspect medication is identified (NSAID, PPI, SSRI, statin…), withdrawing or switching it — under medical supervision — is assessed. Sometimes this single step resolves everything. ^[14]

Step 2: Stop smoking (if applicable)

Smoking is one of the clearest risk factors for this condition. Quitting can meaningfully improve disease course — just one more reason on a very long list.

Step 3: Symptomatic treatment for mild disease

In mild or moderate cases, antidiarrhoeal agents such as loperamide or bismuth subsalicylate may be sufficient to bring symptoms under control. ^[15]

Step 4: Budesonide — the gold-standard treatment

The challenge: relapse rates after stopping are high. For this reason, low-dose maintenance therapy (3–6 mg/day) is considered in patients who keep relapsing. The UEG/EMCG European guidelines are clear on this strategy. ^[13]

What if budesonide doesn't work?

For refractory or budesonide-dependent cases, several options exist: bile acid sequestrants (cholestyramine), immunosuppressants such as azathioprine or methotrexate, and biological therapies including vedolizumab and anti-TNF agents — all showing promising results in case series and smaller trials. ^[10]

Frequently Asked Questions about Microscopic Colitis

Scientific References