Confocal endomicroscopy is a new technology that provides microscopic images of cellular morphology in the gastrointestinal tract in vivo. In particular, confocal microendoscopy allows histological diagnosis during the endoscopic examination. We examined patients with ulcerative colitis (UC) using confocal endoscopy and investigated the features of confocal endomicroscopic images of inflamed and non-inflamed rectal mucosa. Seventeen patients with UC, 12 in the active phase and 5 in the non-active phase, and 14 non-UC control patients who had colon polyps or colon cancer underwent colonoscopy, during which fluorescence images of the rectal mucosa were obtained with confocal endomicroscopy. Histological findings of rectal biopsy specimens were compared with the microendoscopic images. Confocal microendoscopy allowed observation of cellular and subcellular structures. The crypts of normal colonic mucosa were small, round and regularly arranged, and the crypt lumens of the colonic glands were small and round. The crypts of colonic mucosa in non-active UC were small, round and slightly irregular in arrangement and the crypt lumens of the colonic glands were small and round. Inflammatory cells and capillaries were visible in the lamina propria. The crypts of colonic mucosa in active UC were large, variously shaped and irregular in arrangement. The crypt lumens of the colonic glands were large and the crypt structure could not be recognized in some areas. Numerous inflammatory cells and capillaries were visible in the lamina propria. Images taken with the confocal microendoscope provided information that was equivalent to conventional histology, and improve our understanding of the differences in rectal tissues (crypts, capillaries and inflammatory cells) between normal controls and active and non-active UC patients during ongoing endoscopy.