Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders, affecting approximately 5-20% of women of reproductive age. PCOS is a multifactorial, complex, and heterogeneous disease, characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovaries, which may lead to impaired fertility. Besides the reproductive outcomes, multiple comorbidities, such as metabolic disturbances, insulin resistance, obesity, diabetes, and cardiovascular disease, are associated with PCOS. In addition to the clear genetic basis, epigenetic alterations may also play a central role in PCOS outcomes, as environmental and hormonal alterations directly affect clinical manifestations and PCOS development. Here, we highlighted the epigenetic modifications in the multiplicity of clinical manifestations, as well as environmental epigenetic disruptors, as intrauterine hormonal and metabolic alterations affecting embryo development and the adulthood lifestyle, which may contribute to PCOS development. Additionally, we also discussed the new approaches for future studies and potential epigenetic biomarkers for the treatment of associated comorbidities and improvement in quality of life of women with PCOS.