Endometriosis involving the mucosa of the intestines is rare, but may lead to diagnostic pitfalls. We reviewed 15 cases (seven biopsies and eight resections) from 14 patients. The patients' mean age is 48 years (31-66 years). Presenting symptoms included lower gastrointestinal bleeding, pelvic pain, rectal urgency, abdominal mass, and bowel obstruction. In the majority of cases, the lesion was located in the rectum (73%) with the remainder in the sigmoid colon (20%) and ileum (7%). The most common indication for biopsy was a polypoid lesion seen endoscopically (eight cases). For patients who underwent resections, the most common clinical impression was colonic carcinoma (75%), due to mass lesions and stricture as the most common macroscopic findings. Histologically, one case had stromal endometriosis only, but the remaining 14 cases had both endometrial glands and stroma. Epithelial metaplasia was present in all cases, mostly tubal metaplasia (ciliated epithelium). Hybrid glands and replacement of the surface epithelium by endometrial epithelium were also seen. Crypt architectural distortion, cryptitis, and crypt abscesses were seen in some cases, mimicking chronic active colitis or enteritis. A panel of immunohistochemical stains (CK7, CK20, CDX2, and ER) was found to be useful in biopsies with suspected endometriosis demonstrating unusual histology or only containing endometrioid stroma tissue. Vascular involvement by endometriosis was identified in one case. Endometrial hyperplasia (n=2) and cancer (n=1) were also seen in the ectopic tissue. All patients were alive at follow-up (3-216 months, mean 67 months).