A review of the current literature was attempted in order to determine to what degree new technological features, such as the use of proteomics, genomics, and gene microarrays, have contributed to the elucidation of the specific pathways to the formation of endometriosis as well as to the discovery of potential biomarkers and new treatment strategies. Endometriosis is well described as a condition in which multiple genetic components and still foggy environmental risk factors are important determinants of the disease's origin, maintenance, persistence, and clinical outcome. The concept is that because of the special features and complexity of the disease, endometriosis is ideally suited as a target for genome- and proteome-wide scanning. Reviewing the current literature we found that, apart from the better understanding of the pathophysiology and the metabolic pathways which lead to potential biomarkers for endometriosis, there are still issues to be clarified and applications to be achieved. The evolving genomic and proteomic technologies remain poised to revolutionize the diagnosis and treatment of endometriosis but have not yet lead to a single new therapy or tested biomarker. The reasons have mainly to do with the complex and multifactorial character of the disease itself.