Mesonephric carcinomas (ME) and Female Adnexal Tumors of probable Wolffian Origin (FATWO) are thought to derive from remnants of the Wolffian/mesonephric ducts – anlages of the male reproductive tract. Mesonephric-like carcinomas (MLC) show identical morphology to ME of the cervix, but occur in the uterus and ovary without convincing mesonephric remnants. ME, MLC and FATWO are challenging to diagnose due to their morphologic similarities to Müllerian tumors, resulting in a lack of evidence-based and tumor-specific treatment regimens. In order to identify potential diagnostic biomarkers, we performed whole proteomic analysis on 9 ME/MLC and 56 endometrial carcinomas (EC). ME and MLC proteomes showed significant overlap with few distinguishing protein markers.