This chapter focuses on the non-invasive approaches which largely concentrate on proteomics analyses. Proteins are generated from the genome with signal sequences that direct them to the cell membrane or are secreted in the extracellular environment. Secreted proteins are often post-translationally modified, in particular by glycosylation. These proteins are then released into the interstitial environment where they may enter body fluids such as the blood system and, in the case of endometriosis, be detected in endometrial, peritoneal, or follicular fluids. In most proteomic approaches, mass spectrometry (MS) plays a part in the analyses. Electrospray ionization (ESI) is the most common method for sample introduction into the MS. Matrix assisted laser desorption ionization (MALDI) is also be used as an alternative to ESI. Two-dimensional gel analyses have traditionally been used for the differential analysis of proteomes and differences may be observed and selected visually or using image analysis of scanned gels.