BACKGROUND: Since many patients with intestinal endometriosis present with gastrointestinal symptoms without a history of endometriosis, endoscopic examination of the intestinal tract is initially performed, often leading to a misdiagnosis. METHODS: We reviewed the clinicopathologic findings of 18 samples from 15 patients with intestinal endometriosis who underwent endoscopic biopsy and/or surgical resection to identify diagnostically helpful findings. RESULTS: All 7 biopsy specimens displayed relatively well-defined submucosal lesions, with non-mucinous glands lined by ciliated epithelium and surrounding cellular stroma containing spiral arteriole-like blood vessels. The stroma was immunopositive for CD10 in all cases. All but one specimen exhibited immunopositivity for ER and PR in both glandular and stromal components. In contrast to the overlying normal colonic mucosa, glandular epithelium with endometriosis was immunopositive for cytokeratin (CK) 7, but immunonegative for CK20 in all cases. Three cases were associated with adenocarcinoma in the same or different segments; specifically, two primary rectal adenocarcinomas and one endometrioid adenocarcinoma arising from endometriosis. CONCLUSIONS: The characteristic features of endometrial glands and stroma, including non-mucinous glands without goblet cells, ciliated columnar epithelium, and cellular stroma with spiral arterioles, facilitate the accurate diagnosis of intestinal endometriosis, which can be confirmed by immunohistochemical staining.