We present a patient with chronic watery diarrhea and weight loss, in whom colonoscopic findings were consistent with microscopic colitis, but histopathological examination revealed granulomatous inflammation. A 67-year-old Japanese female with a several year history of chronic watery diarrhea and body weight loss was admitted to our hospital. Her laboratory data showed hypoalbuminemia and high levels of serum immunoglobulin G and C-reactive protein. Colonoscopic findings were grossly normal. Histopathology showed inflammatory cell infiltrates with non-necrotizing granulomas and multinucleated giant cells, indicating that this was not conventional microscopic colitis, lymphocytic colitis or collagenous colitis. After treatment with prednisolone her symptoms and laboratory data improved dramatically, and she went into remission without the necessity of further steroid treatment.