Endometriosis is one of the most commonly encountered benign problems in gynecology. Even though endometriosis appears to predispose to ovarian cancer the progression from atypical epithelial proliferation (atypical endometriosis and metaplasia), to the formation of well-defined borderline tumors and finally to endometrioid ovarian cancer will take several years. To elaborate on the concept of endometriosis as a precursor of some types of ovarian cancer, we present an overview of the pathophysiological and genetic characteristics, common in those two conditions. Furthermore, we present the genetic mutations found in ovarian cancers and we outline the common genetic alterations of endometriosis and ovarian cancer, focusing on the PI3K/Akt/mTOR-signaling pathway.