Polycystic ovarian syndrome is universally the most common endocrinopathy in women of reproductive age. It is characterized by composite clinical phenotypes reflecting the reproductive impact of ovarian dysfunction (androgen excess, oligo-/anovulation, polycystic ovary) and metabolic abnormalities (insulin resistance, obesity) with widely varying symptoms among the affected. Studies have shown a clear pattern of disparity in clinical manifestations of its component phenotypes across ethnic populations. Recent genetic association studies suggested differential genetic background that could contribute to the observed ethnic disparity. We summarize the current status in genetic studies of the disorder in different populations with a focus on ethnicity. Especially, we highlight and discuss the applications of recent developments in DNA sequencing, global transcriptional and epigenetic profiling that could help to unravel the molecular basis of the interethnic difference in the pathogenesis of the syndrome. It is hoped that identification and characterization of population-specific structural genetic and functional genomic patterns could help to not only deepen our understanding of the aetiology but also develop more efficient strategies for treatment and prevention of polycystic ovarian syndrome.