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Many reproductive disorders such as polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and endometriosis, are heterogeneous and complex, combined both genetic and environmental factors.Candidate gene studies have certain limitations with small sample sizes and limited statistical power; few, if any, positive results have been replicated by this strategy.Whole-genome association studies (GWASs) otherwise provide more reliable and unbiased results; GWASs in PCOS and endometriosis represent milestones for genetic study in reproductive medicine, which provide new clues to understand genetic components and pathways in reproductive physiology.