Colitis cystica profunda is a rare and benign lesion characterized by mucus-containing cysts under the mucosa of the colon and rectum. We report a patient with localized colitis cystica profunda of the rectum diagnosed by endoscopic submucosal dissection. Although colitis cystica profunda is benign, it is sometimes indistinguishable from other malignant lesions. So early excision and biopsy make sense.