The exact cause of microscopic colitis is unknown. Several factors may play a role in causing microscopic colitis. However, most scientists believe that microscopic colitis results from an abnormal immune-system response to bacteria that normally live in the colon. Scientists have proposed other causes, including
                
- autoimmune diseases  - medications  - infections  - genetic factors  - bile acid malabsorption
                
Autoimmune Diseases
                
Sometimes people with microscopic colitis also have autoimmune diseasesdisorders in which the bodys immune system attacks the bodys own cells and organs. Autoimmune diseases associated with microscopic colitis include
                
- celiac diseasea condition in which people cannot tolerate gluten because it damages the lining of the small intestine and prevents absorption of nutrients. Gluten is a protein found in wheat, rye, and barley.  - thyroid diseases such as      - Hashimotos diseasea form of chronic, or long lasting, inflammation of the thyroid.    - Graves diseasea disease that causes hyperthyroidism. Hyperthyroidism is a disorder that occurs when the thyroid gland makes more thyroid hormone than the body needs.    - rheumatoid arthritisa disease that causes pain, swelling, stiffness, and loss of function in the joints when the immune system attacks the membrane lining the joints.  - psoriasisa skin disease that causes thick, red skin with flaky, silver-white patches called scales.
                
More information is provided in the NIDDK health topics:
                
- Celiac Disease  - Hashimotos Disease   - Graves Disease
                
Medications
                
Researchers have not found that medications cause microscopic colitis. However, they have found links between microscopic colitis and certain medications, most commonly
                
- nonsteroidal anti-inflammatory drugs such as aspirin, ibuprofen, and naproxen  - lansoprazole (Prevacid)  - acarbose (Prandase, Precose)  - ranitidine (Tritec, Zantac)  - sertraline (Zoloft)  - ticlopidine (Ticlid)
                
Other medications linked to microscopic colitis include
                
- carbamazepine  - clozapine (Clozaril, FazaClo)  - dexlansoprazole (Kapidex, Dexilant)  - entacapone (Comtan)  - esomeprazole (Nexium)  - flutamide (Eulexin)  - lisinopril (Prinivil, Zestril)  - omeprazole (Prilosec)  - pantoprazole (Protonix)  - paroxetine (Paxil, Pexeva)  - rabeprazole (AcipHex)  - simvastatin (Zocor)  - vinorelbine (Navelbine)
                
Infections
                
Bacteria. Some people get microscopic colitis after an infection with certain harmful bacteria. Harmful bacteria may produce toxins that irritate the lining of the colon.
                
Viruses. Some scientists believe that viral infections that cause inflammation in the GI tract may play a role in causing microscopic colitis.
                
Genetic Factors
                
Some scientists believe that genetic factors may play a role in microscopic colitis. Although researchers have not yet found a gene unique to microscopic colitis, scientists have linked dozens of genes to other types of inflammatory bowel disease, including
                
- Crohns diseasea disorder that causes inflammation and irritation of any part of the GI tract  - ulcerative colitisa chronic disease that causes inflammation and ulcers in the inner lining of the large intestine
                
More information is provided in the NIDDK health topics:
                
- Crohns Disease  - Ulcerative Colitis
                
Bile Acid Malabsorption
                
Some scientists believe that bile acid malabsorption plays a role in microscopic colitis. Bile acid malabsorption is the intestines inability to completely reabsorb bile acidsacids made by the liver that work with bile to break down fats. Bile is a fluid made by the liver that carries toxins and waste products out of the body and helps the body digest fats. Bile acids that reach the colon can lead to diarrhea.