Peritoneal fluid is a specific microenvironment. It originates mainly as an ovarian exudation product due to increased vascular permeability, and contains large amounts of macrophages and their secretion products, which include growth factors, cytokines and angiogenic factors. Similarly, within the ovary, there is also a specific microenvironment, best characterised by the follicular milieu with steroid hormone concentrations that are 1,000 times higher than in plasma. Since endometrial cells in peritoneal fluid and superficially implanted cells will be influenced by peritoneal fluid concentrations, any differences found between minimal endometriosis and eutopic endometrium could be the consequence of their different local environments, rather than inherent cellular differences. Superficial endometrial implants may be regulated by factors in peritoneal fluid, while deep endometriosis and cystic ovarian endometriosis may be under the influence of factors in blood and within the ovary, in which case minimal endometriosis may be physiologic only, while deep endometriosis and cystic ovarian endometriosis, both associated with pelvic pain and infertility, may be a pathological state. In conclusion, the local endocrine environment, that is, in blood, peritoneal fluid, and within the ovary, should be taken into account to explain the differences between superficial, deep and cystic ovarian endometriosis, together with inherent differences in the endometrial cells of women with and without endometriosis.