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Microscopic colitis is a common inflammatory disease of the large intestine, responsible for chronic secretory diarrhea. It is caused by an inappropriate immune response triggered by pharmacological and/or environmental factors. The diagnosis of microscopic colitis relies on histological assessment of colonic biopsy samples. Microscopic colitis is either categorized into collagenous or lymphocytic colitis. The mainstay of treatment involves budesonide and the withdrawal of harmful drugs. The benefits of immunomodulators and biological agents in refractory microscopy colitis is currently emerging in patients with resistance or intolerance to budesonide. A better understanding of the immune response in disease pathogenesis may lead to new therapeutic strategies in the years to come.