Microscopic colitis is a type of inflammatory bowel disease (IBD). It is formally classified alongside Crohn’s disease and ulcerative colitis as an IBD, though it behaves quite differently from both. It causes chronic inflammation in the colon that can only be seen under a microscope, which is why biopsies during a colonoscopy are the only way to diagnose it. If you have microscopic colitis, you have IBD, but a form that is generally less severe and less likely to cause complications than its better-known counterparts.
How Microscopic Colitis Differs From Crohn’s and UC
The biggest distinction is visibility. In Crohn’s disease and ulcerative colitis, a doctor can see obvious damage during a colonoscopy: ulcers, redness, swelling. In microscopic colitis, the colon lining looks completely normal to the naked eye. The inflammation only shows up when a pathologist examines tissue samples under a microscope. This is why it went unrecognized for decades and why some people still aren’t sure it “counts” as IBD.
The differences go deeper than appearance. Crohn’s disease can strike anywhere in the digestive tract and burrow through multiple layers of tissue. Ulcerative colitis causes surface ulcers and bleeding. Microscopic colitis produces a different pattern: either an abnormal buildup of white blood cells in the colon lining (lymphocytic colitis) or a thickened band of collagen beneath the surface (collagenous colitis). Neither subtype causes the kind of tissue destruction that leads to strictures, fistulas, or surgical removal of the colon. The NIDDK notes that microscopic colitis is less likely to lead to complications compared with other types of IBD.
Perhaps most reassuring: microscopic colitis does not increase your risk of colon cancer. A retrospective study comparing people with microscopic colitis to the general population found no statistical increase in rates of colorectal cancer, even among those who had multiple flares. This stands in contrast to ulcerative colitis and Crohn’s colitis, where long-standing inflammation does raise cancer risk over time.
Two Subtypes, One Disease
Microscopic colitis comes in two forms. In lymphocytic colitis, pathologists find an elevated number of immune cells (specifically lymphocytes) embedded in the surface of the colon lining. In collagenous colitis, the layer of collagen just beneath the surface grows abnormally thick, sometimes more than double its normal size. A normal collagen band is a few micrometers thick; in collagenous colitis, it measures over 10 micrometers and often reaches 25 or more. Both subtypes produce essentially the same symptoms, and treatment is the same for both.
Symptoms
The hallmark symptom is chronic, watery diarrhea without visible blood. Most people with microscopic colitis have four to nine bowel movements a day, though some exceed ten. Unlike many digestive conditions, the diarrhea frequently strikes at night, disrupting sleep. Other common symptoms include abdominal cramping, urgency, and unintentional weight loss. Because there’s no bleeding and colonoscopy looks normal, many people go months or years before getting the right diagnosis.
Who Gets Microscopic Colitis
Microscopic colitis is most commonly diagnosed in older adults. The median age at diagnosis is 68, and incidence climbs with each decade of life, peaking at roughly 37 cases per 100,000 people annually among those 80 and older. Women are affected more often than men overall, accounting for about 70% of cases. The gender gap is especially pronounced in collagenous colitis, where women are diagnosed at more than four times the rate of men. For lymphocytic colitis, the difference between sexes is much smaller and not statistically significant.
The condition has also become more commonly recognized over time. Population data from Olmsted County, Minnesota showed incidence rising from about 1 case per 100,000 in the early years of tracking to nearly 20 per 100,000 by the study’s end, likely reflecting greater awareness and more routine biopsying during colonoscopy.
Triggers and Risk Factors
Several commonly used medications are associated with an increased risk of developing microscopic colitis. A systematic review and meta-analysis found that people taking proton pump inhibitors (drugs like omeprazole used for acid reflux) had roughly 2.7 times the odds of developing the condition. SSRIs, a widely prescribed class of antidepressants, carried about twice the risk. NSAIDs like ibuprofen and naproxen showed a similar doubling of risk, and statins were associated with about 1.7 times the odds.
This doesn’t mean these medications cause microscopic colitis in every person who takes them, but the association is strong enough that doctors often evaluate a patient’s medication list as part of the workup. In some cases, stopping the offending drug resolves the diarrhea entirely. Microscopic colitis is also linked to other autoimmune conditions, particularly celiac disease, thyroid disorders, and rheumatic diseases, suggesting an underlying immune-mediated process in many patients.
How It’s Diagnosed
Because the colon looks normal during a standard colonoscopy, diagnosis depends entirely on biopsies. A flexible sigmoidoscopy (which only examines the lower part of the colon) is often inadequate. A full colonoscopy with biopsies taken from multiple locations is the standard approach. Gastroenterologists typically collect tissue samples from both the right and left sides of the colon, since inflammation can vary by location and these regions have different embryologic origins. The samples are placed in separate containers so the pathologist can evaluate each segment independently. This targeted biopsy strategy is the only reliable way to confirm the diagnosis.
Treatment and Outlook
The first-line treatment is budesonide, a locally acting steroid that targets the gut while minimizing the systemic side effects of other steroids. It is highly effective. In randomized trials, 77% to 96% of patients achieved remission within six to eight weeks on a standard dose, compared to 12% to 20% on placebo. The medication works for both collagenous and lymphocytic colitis.
The catch is relapse. Many people experience a return of symptoms after stopping budesonide, so some need a low maintenance dose to stay symptom-free. Dietary adjustments can help as a complement to treatment. Limiting or avoiding alcohol, caffeine, artificial sweeteners, and dairy (if lactose intolerant) may reduce symptom severity. If you also have celiac disease, a gluten-free diet is particularly important.
For people whose microscopic colitis was triggered by a specific medication, removing that medication sometimes resolves symptoms without any other treatment. This makes a thorough medication review one of the most important early steps in management.