Deep endometriosis has been defined as endometriosis infiltrating deeper than 5 mm under the peritoneum. A model for the development and propagation of endometriosis is presented. Subtle and non-pigmented lesions are suggested to occur intermittently in all women. Infiltration occurs generally to a few millimeters of depth only, and these lesions become typical, burnt out lesions. In some 20% of women, severe endometriosis develops either as deeply infiltrating disease or as cystic ovarian disease. Arguments are given to consider deep endometriosis and cystic ovarian endometriosis as two specific entities of endometriotic disease. A possible causal relationship with dioxin pollution is discussed. Diagnosis of deep endometriosis is made by clinical examination and palpation during surgery. Clinical examination during menstruation and CA-125 concentrations in plasma are useful to help in the diagnosis of smaller deep lesions. Surgical excision can be carried out by laparoscopy, laparotomy or vaginally using sharp dissection, electrosurgery or with the use of a CO2 laser. Excision is the treatment of choice because of a high pregnancy rate, a complete cure of pain in most women, and a low recurrence rate. Medical treatment is probably less effective to treat infertility, but highly effective in relieving pelvic pain. Medical therapy, by luteinizing hormone-releasing hormone agonists, danazol, or gestrinone, also seems useful as a pretreatment for surgery. The choice of treatment will therefore depend on the local expertise with minimal invasive surgery, certainly if a first excision has been incomplete and pain symptoms recur.