Endometriosis has a high prevalence (10 to 15% of the reproductive age women) and can cause pelvic pain and infertility. Because of the complexity involved in diagnosing and treating this disease, in the nineties the study of endometriosis became the target of strategic modifications, that were reinforced after the observation that the disease must be evacuated according to its depth, as described in 1990 and 1992. Nodules of endometriosis with depth of 5 or more millimeters are defined as deep endometriosis and it can affect the pouch of Douglas, retrocervical area, bladder, ureter, intestinal wall and, less frequently, the rectovaginal septum. Those constitute the most severe form of endometriosis, considered an invasive disease. This chapter discusses the specific treatment of deep endometriosis. Deep endometriosis requires a thorough preoperative investigation and appropriate, subsequent surgical planning. It is imperative to perform a careful, thorough and critical preoperative analysis of the clinical data and the findings of the various imaging techniques used to plan the appropriate treatment and surgical approach and avoid the surgical team to face a situation it is unable to resolve satisfactorily. Thereafter, the surgical approach for the various parts of the procedure will depend on the symptoms of the patient and the extent of invasion of each organ involved by the disease. The surgical team must be multidisciplinary, composed of gynecologists, urologists and digestive tract surgeons, as necessary, since all visible and palpable lesions of the disease must be excised for the patient to reap any real benefits, bearing in mind that the concept of “one shot surgery” is the best option to avoid persistence of lesions and minimize the rate of recurrence of the disease following surgery.