Peritoneal and ovarian endometriosis are characterized by chronic bleeding, leading to the formation of hemorrhagic blisters, fibrosis, adhesions, and ovarian endometriomas. Endometriosis is further distinguished by altered immune cell responses, inflammation, neoangiogenesis, and ovarian and uterine dysfunction. In the near future, however, new arising technologies, for instance transcriptomics and proteomics, could also be used for the non-invasive diagnosis of endometriosis. This review centers on recent studies which assess imaging and proteomic techniques, and describe the novel molecular markers currently being developed for the diagnosis of endometriosis. The new imaging and “omics” techniques will be able to improve our understanding and early detection of endometriosis and the search for future candidates for endometriosis treatment. Once a gene/protein, or a small number of genes/proteins, has been shown to be differentially expressed in endometriosis, the next step will be to use this information in an attempt to develop a non-invasive diagnostic test for endometriosis. Ideally, this diagnostic test should display good sensitivity and specificity as well as satisfactory positive and negative predicative values for the detection of endometriosis, and should also be cost-effective and readily available.