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Abstract Introduction Intussusception of the appendix is an extremely rare condition that ranges from partial invagination of the appendix to involvement of the entire colon. Endometriosis is an exceptionally rare cause of appendiceal intussusception and only very few cases have been reported in the literature to date. Case presentation A 40 year-old woman presented to clinic with a long history of lower abdominal pain, loose motions and painful, heavy periods. Subsequent colonoscopy revealed submucosal endometriotic nodules in the sigmoid as well as a polyp thought to be arising from the appendix, which had inverted itself. She was referred to a colorectal surgeon because the polyp could not be removed endoscopically despite several attempts. At laparotomy, the appendix had intussuscepted but it was possible to reduce it and therefore a simple appendicectomy was carried out. On histology, there were widespread endometrial deposits within the wall of the appendix and this was thought to be the basis for the intussusception. Conclusion Histological evidence of the lead point is of crucial importance in cases of appendiceal intussusception, in order to exclude an underlying neoplastic process. Consequently, surgical resection is necessary either through an open or a laparoscopic approach. Gastrointestinal endometriosis should be considered as a cause of appendiceal intussusception in post-menarchal women with episodic symptoms and proven disease.