Firstly described at the end of nineteenth century, endometriosis remains an enigmatic disease, from etio-pathogenesis to specific markers of diagnosis and its ability to associate with malignancies. Our review has been designed from a historical perspective and steps up to an updated understanding of the disease, facilitated by relatively recent molecular and genetic progresses. Although the histopathological diagnosis is relatively simple, the therapy is difficult or ineffective. Experimental models have been extremely useful as they reproduce the human disease and allow the testing of different potential modulators or treatment options. Due to molecular resemblance to carcinogenesis, applications of anti-cancer agents are currently under scrutiny. The desired goal of an efficient therapy against symptomatic disease, along with associated infertility and malignancies, needs a deeper insight into the complex mechanisms involved in endometriosis initiation, development, and progres-sion. Current trends in genomic and proteomic approaches are useful for a more accurate classification and for the identification of new therapeutic targets.