Polycystic ovary syndrome (PCOS) is a complex disorder causing metabolic disturbances and reduced fertility in women of reproductive age, the definition of which is an on-going debate among researchers in the field. PCOS is characterized by hyperandrogenism, chronic anovulation and glucose homeostasis. It is one of the most common endocrinopathies affecting 5-15% of women of reproductive age worldwide and causes more than 75% of cases of anovulatory infertility. The etiology of PCOS is largely unknown though contains a clear genetic component. However, to date, the only available PCOS genome-wide association data have reported 11 significant loci and come from a study of Han Chinese individuals. We, in the PCOS consortia, that consists of 15+ research teams, are gearing up to perform their first and second waves of genome-wide and also exome-wide association meta-analyses in up to 15,000 cases and 80,000 controls of European decent, as well as extensive pathway analysis and genomic follow-up. The overall aim is to identify genetic variation, transcripts and pathways that are associated with PCOS susceptibility (and related subphenotypes). We will perform case:control analysis for PCOS itself and for some of the related subphenotypes which present as dichotomous outcomes. We will in parallel perform quantitative analysis for subphenotypes that are quantitative traits. We will adjust for standard confounders like age and also investigate what effect related phenotypes like BMI have on the PCOS results by performing both adjusted and unadjusted analysis. The genetic and genomic discovery paired with biologic follow-up, holds the promise of bridging and linking knowledge from the metabolic and gynecologic disease fields and yield clinically useful information.