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Appendiceal or cecal endometriosis with intestinal metaplasia is uncommon and may mimic mucinous tumors of the appendix. A 50-year-old woman was found incidentally to have an ileocecal lesion. In the intraoperative histological examination, a diagnosis of neoplasm of the cecum was made predominantly based on mucin extrusion with scattered lining mucinous epithelium. However, postoperative histological diagnosis of the lesion was cecal endometriosis with intestinal metaplasia as determined by thoroughly microscopic inspection and the presence of typical endometrial glands with surrounding endometrial-type stroma. There was no evidence of recurrence and pseudomyxoma peritonei after 1 year of follow-up. Overinterpretation of cytological atypia or mucin extrusion in endometriosis may lead to inappropriate surgical management. Therefore, in any ileocecal or appendiceal lesions with mucinous epithelia and mucin extrusions, removal of sufficient tissue from different portions of the lesion is essential for surgeons and pathologists to make a precise diagnosis in the intraoperative histological examination.