Polycystic ovary syndrome (PCOS) is a hormonal disorder common among women of reproductive age. PCOS is characterized by ovarian dysfunction and metabolic abnormalities with widely varying clinical manifestations brought about by intricate mechanisms of interplay between the genome and the environment. The popularity of epigenome-wide association studies (EWASs) is helping to facilitate the discovery of environment-mediated molecular modification in PCOS from disease etiology to epigenetic marker discovery. Current epigenetic studies have provided convincing observational evidence linking epigenetic regulation with PCOS origin, manifestation, clinical heterogeneity and comorbidity, which could lead to improved management of the disease through efficient intervention and prevention strategies. Several biological pathways have been consistently reported by independent studies, revealing functional regulation due to endocrine abnormalities and metabolic dysfunction in PCOS, while also suggesting an autoimmune component in the condition. The use of high-throughput sequencing technologies for analysing the epigenome integrated with causal inferences is expected to facilitate effective and efficient PCOS management to promote reproductive health.