Purpose Gastrointestinal involvement of endometriosis may exist in up to 37% of women suffering from endometriosis, but malignant transformation of intestinal endometriosis is extremely rare. In this case report, we present a case of endometrioid adenocarcinoma arising from 2 different large bowel endometriotic sites, with a review of the reported cases of epithelial malignancies developed in gastrointestinal endometriosis. Case A 33-year-old nulligravid Japanese woman was admitted for the evaluation of massive ascites. The patient had undergone a laparoscopic bilateral cystectomy for bilateral endometriomas 8 years before. At laparotomy, we found massive serous ascites, diffuse peritoneal endometriotic lesions, edematous gastrointestinal tract with small surface nodules, stenosis of the sigmoid colon and firm and thick peritoneum. No endometriotic or tumorous lesions were found in the genital tract. The patient underwent a resection of the sigmoid colon, partial resection of the transverse colon, partial omentectomy and multiple biopsies of the peritoneum and ovaries. On the histologic examination, benign endometriosis, atypical hyperplasia and grade 1 endometrioid adenocarcinoma were found to be present in the transverse and sigmoid colon. Subsequently, the patient was treated with chemotherapy consisting of paclitaxel and carboplatin under a diagnosis of endometrioid adenocarcinoma arising in the intestinal endometriosis. The patient is well without evidence of disease 26 months following the surgery. Conclusions The tumors arising from intestinal endometriosis can clinically and pathologically mimic primary neoplasms of the gastrointestinal tract. Recognition of these lesions is important because primary gastrointestinal neoplasms are managed differently from those arising in endometriosis, and these differences may have significant clinical implications.