Microscopic Colitis: Understanding Your Pathology Report

by Catherine Forse MD FRCPC
March 30, 2026

Microscopic colitis is a non-cancerous condition in which immune cells accumulate in the inner lining of the colon, causing inflammation and damage. This inflammation interferes with the colon’s ability to absorb water, leading to persistent watery diarrhea. The condition is called “microscopic” because the colon looks entirely normal during a colonoscopy — the changes can only be seen when tissue is examined under a microscope.

Microscopic colitis is not cancer and does not increase the risk of developing cancer. It is divided into two types based on what the pathologist sees under the microscope: lymphocytic colitis and collagenous colitis. Both types cause the same symptoms and are treated similarly. This article explains what microscopic colitis is and how it is diagnosed. For detailed information about each type, see the dedicated articles linked above.

What are the symptoms?

The hallmark symptom of microscopic colitis is chronic watery diarrhea that can last for weeks, months, or even years. The diarrhea can be frequent and significantly disruptive to daily life. Other symptoms may include abdominal cramping or pain, bloating, unintentional weight loss, and fatigue.

Symptoms often come and go, with periods of flare alternating with periods of relative improvement. Because these symptoms overlap with other digestive conditions — including irritable bowel syndrome and inflammatory bowel disease — microscopic colitis is sometimes not diagnosed until other causes have been investigated and ruled out. A colonoscopy with biopsies is the only way to confirm the diagnosis.

Who is affected?

Microscopic colitis is more common in middle-aged and older adults, typically those over fifty. Collagenous colitis affects women significantly more often than men. Lymphocytic colitis affects men and women at similar rates. Overall, microscopic colitis is one of the more common causes of chronic watery diarrhea in older adults, though it remains relatively uncommon compared to conditions such as irritable bowel syndrome.

What causes microscopic colitis?

The exact cause is not fully understood and likely involves a combination of factors. Several contributing causes have been identified:

  • Medications. Certain drugs are strongly associated with microscopic colitis and can trigger or worsen both types. The most commonly implicated include non-steroidal anti-inflammatory drugs (NSAIDs such as ibuprofen and naproxen), proton pump inhibitors (such as omeprazole and pantoprazole), selective serotonin reuptake inhibitors (SSRIs, a class of antidepressants), and olmesartan (a blood pressure medication). If a medication is identified as a trigger, stopping it often leads to significant improvement or complete resolution of symptoms.
  • Autoimmune response. The immune system appears to play a central role. A leading theory is that immune cells mistakenly attack the cells lining the colon, triggering chronic inflammation.
  • Changes in gut bacteria. Alterations in the normal bacterial environment of the colon may trigger an abnormal immune response in some people.
  • Smoking. Smoking is associated with a higher risk of microscopic colitis, particularly collagenous colitis. Quitting smoking is generally advisable and may reduce symptom severity.
  • Genetic factors. Some people may have a predisposition to developing microscopic colitis, though the specific genes involved are not yet well established.

In many cases, no single clear trigger is found, and the condition is managed based on symptoms rather than an identified cause.

How is the diagnosis made?

Because microscopic colitis produces no visible changes in the colon, the diagnosis cannot be made solely from a colonoscopy. If your doctor suspects microscopic colitis based on your symptoms, they will recommend a colonoscopy during which small tissue samples called biopsies are taken from several different parts of the colon. Taking biopsies from multiple locations is important because microscopic colitis can be patchy — affecting some areas of the colon but not others — and a single biopsy could miss it.

The tissue is sent to a pathologist, who examines it under a microscope. The pathologist identifies the type of microscopic colitis based on the specific features present in the tissue.

What does the pathology report describe?

The pathologist looks for two distinct patterns of change, each corresponding to one type of microscopic colitis. Both types share some features but differ in one important way.

Lymphocytic colitis

In lymphocytic colitis, the defining feature is an abnormally large number of immune cells called lymphocytes within the colon’s surface lining — a pattern called intraepithelial lymphocytosis. These lymphocytes are found both within the glands (crypts) and in the lamina propria, the supportive tissue just beneath the surface. Over time, the lymphocytes damage the glands, causing them to shrink — a process called atrophy — and produce less mucin, which impairs the colon’s ability to function normally.

Collagenous colitis

Collagenous colitis shares all the same inflammatory features as lymphocytic colitis — including increased lymphocytes and gland damage — but has one additional defining feature: a thickened band of collagen, a structural protein, that forms just beneath the surface lining of the colon. This collagen band is absent in lymphocytic colitis, and its presence distinguishes the two types. Pathologists sometimes use a special stain called Masson’s trichrome to highlight the collagen band and confirm the diagnosis.

How microscopic colitis differs from inflammatory bowel disease

Both microscopic colitis and inflammatory bowel disease (IBD) cause chronic inflammation in the colon, but they are distinct conditions with different patterns of damage. In IBD — including ulcerative colitis and Crohn’s disease — the glands become distorted and irregular in shape, a change called crypt distortion, and inflammation can extend into deeper layers of the colon wall. These features are not seen in microscopic colitis. The absence of crypt distortion and deep-wall inflammation is part of what allows the pathologist to confirm microscopic colitis rather than IBD. To learn more, see our article on chronic colitis.

What happens next?

Microscopic colitis is a treatable condition, and most people experience significant improvement with appropriate management. The approach is broadly the same for both lymphocytic and collagenous colitis.

The first step is to review any medications that may be contributing to the condition. If a drug such as an NSAID, proton pump inhibitor, SSRI, or olmesartan is identified as a likely trigger, stopping or changing it can lead to substantial improvement or even complete resolution of symptoms.

When medication adjustment is insufficient, or no trigger is identified, the most effective treatment is budesonide — a corticosteroid that acts locally in the colon with minimal whole-body absorption. Most people respond well to a short course. Other options include bismuth subsalicylate, cholestyramine, and dietary adjustments, such as reducing caffeine, alcohol, or dairy intake. In more persistent cases, a gastroenterologist may consider immunosuppressant or biologic therapies.

Many people experience periods of spontaneous improvement, and some go into remission without active treatment. Relapses are common, however, and ongoing follow-up is important. Regular surveillance colonoscopies are not typically needed, since microscopic colitis does not increase the risk of colorectal cancer.

For detailed information on treatment and follow-up for each type, see the articles on lymphocytic colitis and collagenous colitis.

Questions to ask your doctor

  • What type of microscopic colitis do I have — lymphocytic or collagenous?
  • Could any of my current medications be contributing to this condition?
  • What treatment do you recommend, and how long will I need to take it?
  • What should I do if my symptoms return after finishing treatment?
  • Are there dietary or lifestyle changes that might help manage my symptoms?
  • Will I need follow-up colonoscopies, and if so, how often?
  • Should I be referred to a gastroenterologist if I am not already seeing one?

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Disclaimer: The articles on MyPathologyReport are intended for general informational purposes only and do not address individual circumstances. They are not a substitute for professional medical advice, diagnosis, or treatment. Never ignore professional medical advice in seeking treatment because of something you have read on the MyPathologyReport site.

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