Polycystic ovary syndrome (PCOS) is a common heterogeneous endocrinopathy, of unknown aetiology affecting women in reproductive age. The syndrome remains an unravelled mystery from the definition to the pathogenesis, long term metabolic sequalae and management. The last decade, a great spectrum of several metabolic aberrations has been linked to defective insulin action in this syndrome. The majority of recent data suggest that there is a post-receptor signalling defect on insulin action in target tissues and the molecular studies have been steadily expanding in an effort to shed some light in the pathogenesis of this multifaceted syndrome. Additionally genomic variants related to insulin resistance and hyper-insulinemia have been found in association with PCOS influencing the metabolic abnormalities. In this review an effort will be made to cover the spectrum of metabolic abnormalities present in the syndrome and mainly to focus on the molecular and genetics defects linked with the pathogenesis of insulin resistance in this disorder.