Microscopic Colitis: The Inflammation a Standard Colonoscopy Can Miss

For many people with chronic, watery diarrhoea, a colonoscopy comes back “normal”, and that can feel more frustrating than reassuring. The bowel lining looks healthy to the naked eye, yet the symptoms persist, sometimes for months before an answer is found. This is often the experience of people with microscopic colitis, a form of bowel inflammation that is invisible unless tissue samples are examined closely under a microscope.

What is microscopic colitis?

Microscopic colitis is a type of inflammatory bowel disease (IBD) in which the lining of the large bowel (colon) becomes inflamed at a cellular level, but shows no visible ulcers, redness, or structural changes during a standard colonoscopy. The only way to detect it is through a biopsy, where small tissue samples are taken and examined under a microscope. There are two main subtypes: lymphocytic colitis, where excess white blood cells called lymphocytes build up in the bowel lining, and collagenous colitis, where a thickened band of collagen (a structural protein) forms beneath the surface layer of the bowel. Both cause chronic watery diarrhoea, often without blood, and typically affect people over the age of 50, with women more commonly diagnosed than men.

Why it matters for gut inflammation

Although microscopic colitis is structurally different from Crohn’s disease or ulcerative colitis, it shares the same underlying theme: the immune system becomes inappropriately activated in the gut lining, disrupting the bowel’s ability to absorb water and maintain a stable barrier. This matters because unresolved, low-grade inflammation, even when invisible on standard imaging, can still produce significant daily symptoms, nutritional strain, and reduced quality of life if it is not identified and managed appropriately.

Key mechanisms

Immune cell infiltration

In lymphocytic colitis, an increased number of lymphocytes gather within the surface lining of the colon. This immune activity interferes with the bowel’s normal fluid-absorbing function, which is a major reason why watery diarrhoea is the dominant symptom rather than cramping or visible blood.

Collagen deposition

In collagenous colitis, the body lays down an abnormally thick band of collagen just beneath the surface cells of the bowel. This thickened layer acts as a physical barrier, reducing how efficiently water and electrolytes are absorbed back into the body, which again drives chronic diarrhoea.

Medication triggers

Certain medications are strongly associated with microscopic colitis, particularly nonsteroidal anti-inflammatory drugs (NSAIDs, a group of painkillers that includes ibuprofen), proton pump inhibitors (drugs used to reduce stomach acid), and some antidepressants. These medications may trigger or worsen the immune response in susceptible individuals, although not everyone who takes them will develop the condition.

Bile acid malabsorption

Bile acids are substances produced by the liver to help digest fat. In some people with microscopic colitis, bile acids are not properly reabsorbed in the small bowel and pass into the colon in excess, where they can irritate the lining and contribute further to diarrhoea. This overlap means some patients benefit from treatments that specifically target bile acid handling.

Autoimmune associations

Microscopic colitis is more common in people who also have other autoimmune conditions, such as coeliac disease (an immune reaction to gluten) or thyroid disorders. This suggests a shared underlying tendency towards immune dysregulation, where the immune system mistakenly targets the body’s own tissues, rather than microscopic colitis being an isolated bowel problem.

Symptoms, inflammation, and medical care

It is important to understand that chronic diarrhoea does not always mean active inflammation, and symptoms can sometimes persist even after inflammation has settled, due to changes in bowel sensitivity or function. Equally, inflammation can occasionally be present without dramatic symptoms. This is why biopsy-confirmed diagnosis, and ongoing review with a gastroenterologist, remains essential rather than relying on symptom patterns alone. Dietary and lifestyle approaches may support overall gut stability, but they are not a substitute for medical assessment, appropriate testing, or prescribed treatment, which commonly includes budesonide (a corticosteroid that acts mainly within the gut) as a first-line option.

Practical takeaways

• Keep a simple symptom and medication diary, since certain drugs are closely linked to flare patterns in microscopic colitis.
• Ask your doctor whether a colonic biopsy was taken if a previous colonoscopy looked “normal” but symptoms persist.
• Avoid stopping or changing prescribed medication without medical advice, even if you suspect it may be contributing to symptoms.
• Discuss any additional autoimmune symptoms, such as fatigue or joint pain, with your healthcare team, as these may be related.
• Maintain consistent hydration and electrolyte intake during periods of frequent diarrhoea.
• Attend follow-up appointments even after symptoms improve, to monitor for recurrence or related conditions.

Conclusion

Microscopic colitis is a reminder that gut inflammation does not always announce itself visibly, and that a clear colonoscopy does not always mean a clear bowel. Long-term stability depends on accurate diagnosis through biopsy, consistent monitoring, and working closely with a gastroenterologist to manage contributing factors such as medication use. While the condition can be frustrating to diagnose, it generally responds well to appropriate medical treatment over time. Understanding the mechanisms involved can help patients feel more informed and less alone when navigating a diagnosis that is often overlooked. This article does not replace individualised medical care, and ongoing symptoms should always be discussed with a qualified healthcare professional.

References

1. Pardi DS. Diagnosis and management of microscopic colitis. Am J Gastroenterol. 2017;112(1):78-85. doi:10.1038/ajg.2016.477.
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3. Nguyen GC, Smalley WE, Vege SS, et al. American Gastroenterological Association Institute guideline on the medical management of microscopic colitis. Gastroenterology. 2016;150(1):242-246. doi:10.1053/j.gastro.2015.11.008.
4. Bohr J, Tysk C, Eriksson S, et al. Collagenous colitis: a retrospective study of clinical presentation and treatment in 163 patients. Gut. 1996;39(6):846-851. doi:10.1136/gut.39.6.846.
5. Fernández-Bañares F, Esteve M, Salas A, et al. Bile acid malabsorption in microscopic colitis and in previously unexplained functional chronic diarrhoea. Dig Dis Sci. 2001;46(10):2231-2238. doi:10.1023/A:1011927302076.
6. Masclee GMC, Coloma PM, Kuipers EJ, Sturkenboom MCJM. Increased risk of microscopic colitis with use of proton pump inhibitors and non-steroidal anti-inflammatory drugs. Am J Gastroenterol. 2015;110(5):749-759. doi:10.1038/ajg.2015.119.
7. Pardi DS, Loftus EV, Smyrk TC, et al. The epidemiology of microscopic colitis: a population-based study in Olmsted County, Minnesota. Gut. 2007;56(4):504-508. doi:10.1136/gut.2006.105890.

This article is intended for informational and educational purposes only. It does not constitute medical advice and should not be used as a substitute for professional medical guidance, diagnosis, or treatment.

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