Endometriosis is a pathological condition defined by the occurrence of endometrial glandular and stromal structures in anatomical compartments different from the uterine cavity. Endometriosis is a genetic polymorphism, estrogen-dependent inflammatory disease. This very common pathological entity causes a high level of morbidity in patients; it is also considered one of the most important causes of infertility. We and others have proposed as a pathogenetic mechanism of endometriosis a modification in the fine tuning of the processes of organogenesis of the uterus. We have correlated the immunohistochemical expression in deep endometriotic lesions and in normal endometrial tissue of several molecular factors that are implicated in the embryonic development of the uterine glands. We noticed a significant higher expression both for epithelium and stroma in the controls respect to the endometriosis samples for FGF7, FGF-10 and HGF. Interestingly, regarding FGF-23 and IFN-τ, we observed a significant higher expression in the ectopic endometrial stroma compared to the eutopic endometrium, while thepithetlium expression did not display a significant differential expression in endometriosis tissues respect to normal endometrium. The data generated support the fact that endometriosis tissues, both the epithelial and stromal component, have a different phenotype respect to the eutopic endometrium and sustain the hypothesis that alterations in the molecular mechanisms in control for adenogenesis and survival of endometrial structures are linked to the genesis and survival of endometriosis lesions outside of the uterus.