Endometriosis is a chronic, nonmalignant and estrogen-dependent disease in which endometrial glandular epithelium and stroma are outside the uterine cavity (ovaries, peritoneum, or rectovaginal septum). The prevalence is estimated from 2 to 10% in women of childbearing age and it rises up to 50% in women with infertility. Despite maximal efforts, the therapy of first choice in the management of endometriosis is still unclear. The aim of this chapter is to present an update of its management, emphasizing the benefits and disadvantages of surgical methods. We performed a systematic literature search on the PubMed database of English literature (search terms: endometrioma, surgery, ovarian reserve, assisted reproductive technologies) from 2010 to 2014. For endometrioma, operative laparoscopy proved to be the gold standard. Surgical procedures consist of partial excision of the cyst wall and electro-coagulation of the rest. Stripping technique may be a better method for reducing the recurrence of pain symptoms, recurrence, and reoperation rates, but it raises concerns about ovarian reserve. For endometriosis, surgery often includes partial rectum or sacrouterine ligament resection. Hysterectomy is not obligatory and refused by the young patients. The approach should be laparoscopic and if necessary vaginal assisted. Good cooperation between various disciplines (gynecology, surgery, urology) is mandatory.