Endometriosis is a frequent gynecological disease of unknown etiology and pathogenesis. It affects the gynecological organs and the peritoneum with varying frequency and can lead to severe symptoms, mainly pain and to infertility. Despite the fact that causal therapy is not feasible diagnostic and therapeutic procedures are necessary in many cases. In a small percentage of cases endometriosis is associated with neoplastic disease and in some cases it might develop into a neoplasm via the stage of atypical endometriosis, notably in the ovaries. Tumors which are most frequently associated with endometriosis are endometrioid carcinoma, clear cell carcinoma, and low grade serous carcinoma. According to some authors tumors associated with endometriosis have a better prognosis than those without. Other tumors are Mullerian adenosarcoma, endometrioid stromal sarcoma, and seromucinous borderline tumor. In addition to the morphological findings more recent molecular findings serve to demonstrate the origin of the different types of carcinoma from endometriosis. In both endometrioid and clear cell carcinoma, loss of heterozygosity (LOH) can be found in different gene loci. Mutations in CTNNB1 (beta catenin), PTEN, KRAS and ARID1a genes have been demonstrated in endometrioid carcinoma. Cases of clear cell carcinoma have been characterized by mutations of ARID1a gene, PIK3CA and less frequently PPP2R1A and KRAS.