Microscopic colitis (MC) is a common cause of unexplainable, chronic diarrhea. The disease is characterized by the presence of clinical symptoms, a normal colonoscopy and typical histopathological changes upon microscopic examination. The aim of the study was to present a case of an atypical histological form of MC. A 56 year-old man presented with chronic, watery diarrhea. Gastrointestinal infection had been excluded. The colon appeared almost normal on the colonoscopy. Inconsistent histological findings were observed. The pathology of randomly taken colon biopsies showed collagenous colitis (CC; thickness of collagen bands > 10 µm, < 20 IELs). Six months later during a follow-up colonoscopy, colonic specimens revealed typical findings of lymphocytic colitis (LC), namely, no thickened subepithelial collagen bands were identified. The authors analyzed the risk factors, diagnosis, treatment response, clinical course and the atypical histological outcomes.