Endometriosis is an important gynecological disease, pathologically defined by the ectopic presence of both endometrial glands and stroma, and clinically associated with pelvic pain and infertility. Our current knowledge of the pathogenesis, pathophysiology of related infertility, and spontaneous evolution is still limited, although endometriosis has been described for many years. Future research in endometriosis needs to focus on pathogenesis studies in the baboon model and on the early interactions between endometrial and peritoneal cells in the pelvic cavity at the time of menstruation. Proteomic and genomic approaches are needed to detect potential differences between eutopic endometrium and myometrium in women with and without endometriosis. Immunomodulatory drugs inhibiting endometriosis-associated pelvic inflammation may offer new medical treatment for endometriosis in the future.