Endometriosis is a benign but aggressive disease. It occurs when shed endometrium from the female reproductive tract grows at a site outside the uterus. The physiological changes in endometriosis-abnormal tissue growth, invasion, and adhesion phenomena-are similar to those seen in tumorous tissues. Although the etiology of endometriosis is not well understood, the disease is widely accepted to result from the ectopic implantation of refluxed menstrual tissues. In addition, immunologic changes, genetic factors, and environmental factors might also affect a woman's susceptibility to develop endometriosis. Thus far, laparoscopic examination is required to confirm the presence of endometriosis; there is no reliable marker for its diagnosis. Many studies are therefore focusing on identifying markers for the diagnosis and follow-up of endometriosis. This chapter provides a systematic review of these studies, including recent findings from our group on the identification of molecules, in serum and/or endometrium, which are associated with the development of endometriosis at different stages. From this research, we hope to be able to suggest how to approach the potential markers. The identification of highly sensitive and specific markers of endometriosis should facilitate the development of accurate and non-invasive techniques for diagnosis and prognosis.