Deep endometriosis is defined as an endometriotic lesion that penetrates the retroperitoneal space for a distance of > or =5 mm. Deep endometriosis is extremely active, occurs in phase with eutopic endometrium, evolves progressively with age, and is most often located in the pouch of Douglas, the rectovaginal septum, the uterosacral ligaments, and occasionally in the uterovesical fold. These lesions are associated with pelvic pain, the intensity of which is proportional to the depth of penetration. It is clear that choice of treatment depends on the location of the endometriotic lesion. In this paper we describe our methods for the initial diagnosis and subsequent treatment of deep endometriosis. These include consultation and clinical examination protocols, use of rectal endoscopic ultrasonography (EUS), magnetic resonance imaging (MRI), and transvaginal ultrasonography techniques in diagnosis and surgical treatment approaches.