Last updated: March 2026
What Is Microscopic Colitis?
Microscopic colitis is a chronic inflammatory condition of the colon (large intestine) that causes persistent, watery, non-bloody diarrhea. Unlike ulcerative colitis and Crohn's disease — the two major forms of inflammatory bowel disease — microscopic colitis does not cause visible inflammation or ulceration of the colon during colonoscopy. The colon looks completely normal to the naked eye. Instead, the inflammation is only visible under a microscope when biopsy specimens taken from the colon lining are examined by a pathologist. This is where the condition gets its name: the colitis is literally "microscopic."
Microscopic colitis is more common than many people realize. According to data from population-based studies, the combined incidence of microscopic colitis is estimated at 10 to 20 new cases per 100,000 people per year, making it comparable in frequency to Crohn's disease and ulcerative colitis. Studies suggest that microscopic colitis accounts for 10% to 20% of cases of chronic watery diarrhea investigated by colonoscopy, highlighting the critical importance of taking biopsies during the evaluation of unexplained diarrhea — even when the colon looks normal.
At Texas Gut Health in Sachse, TX, Dr. Jaison John provides expert evaluation and treatment for patients with microscopic colitis throughout the Dallas-Fort Worth area. Dr. John completed his gastroenterology fellowship at UT Medical Branch, where he served as Chief Fellow, and his internal medicine residency at UT Austin Dell Medical School, where he served as Chief Resident. He holds dual board certifications from the American Board of Internal Medicine in both internal medicine and gastroenterology. His approach to microscopic colitis follows the latest guidelines from the American Gastroenterological Association (AGA) and emphasizes accurate diagnosis through colonoscopy with biopsy and individualized treatment planning.
Types of Microscopic Colitis
Microscopic colitis has two recognized subtypes, distinguished by their characteristic microscopic appearance on biopsy. Despite their histological differences, both subtypes produce similar clinical symptoms and respond to the same treatments. Many experts now consider them to be different expressions of the same underlying disease.
Collagenous Colitis
Collagenous colitis is characterized by the deposition of an abnormally thick band of collagen (a structural protein) beneath the surface epithelium (lining) of the colon. Under normal conditions, the subepithelial collagen band measures less than 5 micrometers. In collagenous colitis, this band is thickened to 10 micrometers or greater — sometimes reaching 30 to 100 micrometers. This thickened collagen band, combined with chronic inflammatory cell infiltration, disrupts the normal absorptive function of the colon and is believed to contribute to the watery diarrhea characteristic of the condition. Collagenous colitis is slightly more common in women than in men and has a peak incidence in the sixth and seventh decades of life.
Lymphocytic Colitis
Lymphocytic colitis is characterized by an increased number of intraepithelial lymphocytes (IELs) — a type of immune cell — within the surface lining of the colon. The diagnostic threshold is typically defined as more than 20 lymphocytes per 100 surface epithelial cells (normal is fewer than 5). Unlike collagenous colitis, there is no thickened collagen band. Lymphocytic colitis has a more even gender distribution than collagenous colitis, though it still has a predilection for older adults.
Incomplete Microscopic Colitis
Some patients present with histological features suggestive of microscopic colitis but do not meet the full diagnostic criteria for either subtype. This is sometimes referred to as "incomplete microscopic colitis" or "microscopic colitis not otherwise specified." These patients may still benefit from treatment with budesonide and should be managed based on their clinical symptoms.
Symptoms of Microscopic Colitis
The hallmark symptom of microscopic colitis is chronic, watery, non-bloody diarrhea. The symptoms typically develop gradually and can range from mildly bothersome to severely debilitating, significantly impacting quality of life.
- Chronic watery diarrhea — Persistent, watery (non-bloody) diarrhea is the cardinal symptom. Patients typically report 4 to 9 watery bowel movements per day, though some experience more than 15 per day in severe cases. The diarrhea is often described as explosive or urgent and may be worse after meals.
- Fecal urgency — A sudden, compelling need to have a bowel movement that is difficult to defer. Fecal urgency is one of the most distressing symptoms and can severely limit social activities and travel.
- Fecal incontinence — Some patients experience involuntary leakage of stool, particularly during episodes of severe urgency. Nocturnal diarrhea (diarrhea that wakes the patient from sleep) occurs in up to 50% of patients.
- Abdominal cramping and pain — Mild to moderate abdominal discomfort, cramping, or bloating is common, though the pain is usually less severe than in other forms of inflammatory bowel disease.
- Weight loss — Chronic diarrhea and impaired colonic absorption can lead to unintentional weight loss, particularly in patients with severe or prolonged symptoms.
- Fatigue — Persistent fatigue and reduced energy are commonly reported and may be related to dehydration, electrolyte imbalances, and the chronic nature of the illness.
- Dehydration — Chronic watery diarrhea can lead to dehydration, manifested by increased thirst, dry mouth, decreased urine output, and dizziness.
- Joint pain — Some patients with microscopic colitis experience arthralgias (joint pain), reflecting the autoimmune associations of the condition.
Important: Microscopic colitis does not cause bloody diarrhea, rectal bleeding, or fever. If you experience bloody stool or fever along with diarrhea, other diagnoses should be considered, and you should seek prompt medical evaluation.
When to See a Doctor
You should see a gastroenterologist if you have chronic watery diarrhea lasting more than 4 weeks, if you are having frequent urgent bowel movements that are interfering with your daily activities, if you have experienced unintentional weight loss, or if you have been treated for irritable bowel syndrome (IBS) but your diarrhea has not responded to typical IBS therapies. Seek prompt evaluation if you develop signs of dehydration (dizziness, dark urine, rapid heart rate), if you have bloody stool, or if you develop fever — these symptoms may indicate a different condition requiring urgent assessment. Contact Texas Gut Health at (214) 624-6596 to schedule your consultation.
Causes & Risk Factors
The exact cause of microscopic colitis is not fully understood, but current evidence suggests that it results from an abnormal immune response in the colon triggered by one or more environmental factors in genetically susceptible individuals. The resulting inflammation disrupts the colon's normal water-absorbing function, leading to watery diarrhea.
Potential Triggers and Contributing Factors
- Medications — Certain commonly used medications have been strongly associated with the development of microscopic colitis. The medications most frequently implicated include:
- Nonsteroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen, naproxen, and aspirin
- Proton pump inhibitors (PPIs) such as omeprazole, lansoprazole, and pantoprazole
- Selective serotonin reuptake inhibitors (SSRIs) such as sertraline
- Statins (cholesterol-lowering medications)
- Acarbose (a diabetes medication)
- Autoimmune associations — Microscopic colitis is associated with an increased prevalence of other autoimmune conditions, suggesting a shared immunological susceptibility. Commonly associated autoimmune conditions include celiac disease (found in 5% to 15% of microscopic colitis patients), thyroid disease (Hashimoto's thyroiditis, Graves' disease), rheumatoid arthritis, type 1 diabetes, and psoriasis. Patients diagnosed with microscopic colitis should be screened for celiac disease with serological testing.
- Bile acid malabsorption — Bile acid malabsorption (BAM), in which excess bile acids reach the colon and stimulate water secretion, is found in a significant proportion of patients with microscopic colitis (estimated at 30% to 60%). BAM may be a contributing mechanism for the watery diarrhea and can be treated with bile acid sequestrants such as cholestyramine.
- Smoking — Current smoking is a well-established risk factor for microscopic colitis. Smokers tend to develop the condition at a younger age and may have more severe symptoms than non-smokers. Smoking cessation is recommended as part of the overall management of microscopic colitis.
Risk Factors
- Age — Microscopic colitis is most commonly diagnosed in adults over the age of 60, with a peak incidence in the sixth and seventh decades of life. However, it can occur at any age.
- Female sex — Women are affected approximately 2 to 3 times more often than men, particularly for collagenous colitis.
- Autoimmune history — A personal or family history of autoimmune conditions increases the risk.
- NSAID or PPI use — Long-term use of these medications is associated with increased risk.
- Smoking — Current smokers have a significantly elevated risk compared to non-smokers.
How Microscopic Colitis Is Diagnosed
The diagnosis of microscopic colitis requires colonoscopy with random biopsies of the colon lining. There is no blood test, stool test, or imaging study that can diagnose microscopic colitis. Because the colon appears completely normal during colonoscopy, the diagnosis is entirely dependent on the histological (microscopic) examination of biopsy specimens.
Colonoscopy with Biopsy
During a colonoscopy, Dr. John visually examines the entire colon. In microscopic colitis, the colonic mucosa typically appears normal or may show only subtle, nonspecific changes such as mild edema or erythema. Because the visual appearance is unremarkable, random biopsies must be taken from multiple sites throughout the colon — typically the ascending (right), transverse, descending (left), and sigmoid colon — to ensure diagnostic accuracy. Taking biopsies from only one location can miss the diagnosis, as the inflammatory changes in microscopic colitis can be patchy and may vary in severity across different segments of the colon.
The biopsy specimens are sent to a pathologist, who examines them under a microscope for the characteristic features of either collagenous colitis (thickened subepithelial collagen band of 10 micrometers or more) or lymphocytic colitis (increased intraepithelial lymphocytes of more than 20 per 100 epithelial cells). The pathologist's report determines both the diagnosis and the subtype.
Laboratory Testing
While no blood test diagnoses microscopic colitis, the following laboratory tests may be performed as part of the evaluation:
- Celiac serologies — Because of the strong association between microscopic colitis and celiac disease, testing for tissue transglutaminase IgA antibodies (tTG-IgA) is recommended.
- Complete blood count (CBC) — To evaluate for anemia or elevated white blood cell count.
- Comprehensive metabolic panel — To assess electrolytes, kidney function, and hydration status.
- C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) — Inflammatory markers that are typically normal or only mildly elevated in microscopic colitis, helping to distinguish it from other inflammatory conditions.
- Stool studies — To rule out infectious causes of diarrhea, including C. difficile infection.
Excluding Other Causes
The differential diagnosis of chronic watery diarrhea is broad and includes irritable bowel syndrome (IBS-D), celiac disease, C. difficile infection, inflammatory bowel disease, medication-induced diarrhea, bile acid malabsorption, small intestinal bacterial overgrowth (SIBO), lactose intolerance, and hyperthyroidism. A thorough evaluation by a gastroenterologist is essential to identify the correct diagnosis and initiate appropriate treatment. Microscopic colitis is frequently misdiagnosed as IBS because the colonoscopy appears normal — underscoring the importance of taking biopsies during the evaluation of chronic diarrhea.
Treatment Options
Treatment for microscopic colitis follows the AGA clinical practice guidelines and is tailored to the severity of symptoms, the impact on quality of life, and each patient's individual response to therapy. The goal of treatment is to achieve clinical remission (resolution of diarrhea) and maintain it over the long term.
Step 1: Identify and Remove Potential Triggers
- Medication review — All current medications should be reviewed to identify potential triggers for microscopic colitis. If an offending medication (such as an NSAID, PPI, or SSRI) is identified, it should be discontinued or substituted when clinically appropriate. In some patients, stopping the offending medication resolves symptoms within 2 to 4 weeks without further treatment.
- Smoking cessation — Patients who smoke should be strongly encouraged to quit, as smoking is a modifiable risk factor that worsens microscopic colitis and may reduce treatment effectiveness.
Step 2: Budesonide (First-Line Medical Therapy)
Oral budesonide is the cornerstone of microscopic colitis treatment and is recommended by the AGA as first-line therapy for patients with clinically significant symptoms. Budesonide is a potent corticosteroid that acts locally in the gut and undergoes extensive first-pass metabolism in the liver, resulting in minimal systemic side effects compared to prednisone or other systemic corticosteroids.
- Induction therapy — Budesonide 9 mg daily for 6 to 8 weeks. Clinical remission (resolution of diarrhea) is achieved in approximately 80% of patients during this induction phase.
- Taper — After the induction phase, budesonide is gradually tapered (typically 6 mg daily for 2 to 4 weeks, then 3 mg daily for 2 to 4 weeks) to reduce the risk of relapse.
- Maintenance therapy — Relapse after discontinuing budesonide is common, occurring in approximately 60% to 80% of patients. For patients who relapse during or after tapering, long-term low-dose maintenance therapy with budesonide (3 to 6 mg daily) is recommended. The AGA supports maintenance budesonide for patients with relapsing microscopic colitis, as it is effective and generally well tolerated. Long-term use requires periodic monitoring for bone density loss (osteoporosis) and other potential side effects.
Step 3: Alternative and Adjunctive Therapies
For patients with mild symptoms or for those seeking to minimize corticosteroid use, the following therapies may be considered:
- Bismuth subsalicylate (Pepto-Bismol) — Bismuth subsalicylate (262 mg, 3 tablets three times daily for 8 weeks) has shown benefit in small studies for mild microscopic colitis. It is well tolerated but may cause black stools and is less effective than budesonide for moderate to severe symptoms.
- Cholestyramine — A bile acid sequestrant that can be effective for patients with concurrent bile acid malabsorption. Cholestyramine (4 g two to three times daily) binds excess bile acids in the colon and can reduce diarrhea. It may be used alone for mild cases or in combination with budesonide.
- Loperamide (Imodium) — An anti-diarrheal agent that can provide symptomatic relief and is often used as an adjunct to other therapies. Loperamide does not treat the underlying inflammation but can help control diarrhea while other treatments take effect.
Step 4: Refractory Microscopic Colitis
For the minority of patients who do not respond adequately to budesonide or who cannot tolerate it, immunomodulatory therapies may be considered:
- Immunomodulators — Azathioprine or methotrexate may be used as steroid-sparing agents for patients with refractory or budesonide-dependent microscopic colitis.
- Biologic therapies — In rare, severe cases that fail all other treatments, biologic agents (such as anti-TNF therapies or vedolizumab) have been used off-label with variable success. Data for biologics in microscopic colitis are limited and come primarily from case series and small studies.
Dietary Modifications
While there is no specific diet proven to treat microscopic colitis, some dietary adjustments may help reduce symptoms:
- Avoid caffeine and alcohol, which can worsen diarrhea.
- Reduce dairy intake if lactose intolerance is suspected.
- Consider a low-fat diet, as dietary fat can worsen bile acid-mediated diarrhea.
- Maintain adequate hydration to replace fluid lost through diarrhea.
- If celiac disease is confirmed, a strict gluten-free diet is essential.