Purpose Endometriosis, a largely benign, chronic inflammatory disease, is an independent risk factor for endometrioid and clear cell epithelial ovarian tumors. We aimed to identify plasma miRNAs that can be used to differentiate endometriosis and ovarian cancer patients from healthy individuals. Experimental design We conducted a two-stage exploratory study to investigate the utility of plasma miRNA profiling to differentiate between endometriosis, endometriosis-associated ovarian cancer (EAOC) and healthy individuals. In the first stage, using global profiling of more than 1,000 miRNAs via reverse transcriptase quantitative PCR (RT-qPCR) in a 20-patient initial screening cohort, we identified 23 candidate miRNAs, which are differentially expressed between healthy controls (n=6), endometriosis (n=7), and EAOC (n=7) patients based on the fold changes. In the second stage, the 23 miRNAs were further tested in an expanded cohort (n=88) of healthy individuals (n =20), endometriosis (n = 33), EAOC (n = 14), and serous ovarian cancer cases (SOC, n= 21, included as controls). Results We identified three distinct miRNA signatures with reliable differential expression between healthy individuals, endometriosis, and EAOC patients. When profiled against the control SOC category, our results revealed different miRNAs, suggesting that the identified signatures are reflective of disease-specific pathogenic mechanisms. This was further supported by the fact that the majority of miRNAs differentially expressed in human EAOC were mirrored in a double transgenic mouse EAOC model. Conclusion Our study reports for the first time that distinct plasma miRNA expression patterns may serve as highly specific and sensitive diagnostic biomarkers to discriminate between healthy, endometriosis, and EAOC cases.