AIM: The aim of this paper is to describe an unique case of deep infiltrating endometriosis of the rectum in non-pregnant woman with unusual clinical and pathological presentation resulting in spontaneous perforation. MATERIALS AND METHODS: A female (20 years of age) with a two year history of chronic recurrent abdominal pain of unknown etiology treated by a psychiatrist underwent diagnostic laparoscopy which revealed many peritoneal implants of endometriosis involving the right ovarian fossa, the vesico-uterine pouch and sacrouterine ligament; the bowel wall showed no structural abnormalities. Peritonectomy of the broad and uterosacral ligaments was used and eight days after the operation, the patient developed crampy abdominal pain and enterorrhagia necessitating laparoscopic revision; pelvic haematoma and rectosigmoiditis were found. Over the next three days, perforation of the rectum resulted in the presence of fecal material in the surgical drain. RESULTS: Lower rectal resection with ileostomy was performed. Microscopic examination revealed discrete small endometriotic lesions in submucosa, muscular layer and serosa of the rectum associated with perforation. DISCUSSION: Laparoscopy and laparotomy may be insufficient in the case of an inactive endometriosis. Definitive diagnosis is thus reached only by the histological examination. The pathophysiology of the bowel perforation secondary to endometriosis is not entirely clear. CONCLUSION: The presented case confirms the importance of interdisciplinary cooperation between surgeons, gynaecologists, and pathologists. We also want to emphasize the need for extensive pathological examination of the resected specimens which is essential for a proper diagnosis.