Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in females of reproductive age, and its prevalence ranges between 6 and 8%. Associated problems include infertility, menstrual disorders, hirsutism and obesity. In addition, individuals with PCOS may be at increased risk of diabetes, endometrial cancer and, possibly, cardiovascular disease and breast cancer in later life. Biomarkers identified from proteomic analyses may help to improve the clinical management of PCOS, provided that new proteomic data can be integrated with existing knowledge and/or pathways implicated in disease etiology. In this study, a database of identity, descriptions and functions/pathways has been developed from 148 published proteomic biomarkers in PCOS. From analysis of the database, a variety of pathways possibly implicated in PCOS were determined, including those related to fibrinolysis, thrombosis, the antioxidant pathway and the immune system. This database, if developed further, will provide a framework for a systems approach to profiling biomarkers in the future.