BackgroundPolycystic ovary syndrome (PCOS) is a common and complex endocrine-metabolic disease. One of the well-documented characteristics of PCOS is obesity or overweightness. It is possible to be genetically predisposed to becoming obese or overweight, and several potentially causative single nucleotide polymorphisms (SNPs), such as rs9939609 (A/T) in the fat mass, and obesity-associated gene (FTO) and rs17782313 (T/C) in the melanocortin-4 receptor gene (MC4R), have been investigated. Further investigation of association between obesity-associated SNPs and PCOS susceptibility will contribute to a better understanding of the disease.MethodsIn the present study, we enrolled 733 patients with PCOS and 892 control subjects. The common variants FTO rs9939609 and MC4R rs17782313 were genotyped and their relationship with obesity-related traits was evaluated.ResultsRs9939609 and rs17782313 are associated with PCOS and obesity-related traits and profiles. The association found between PCOS and FTO rs9939609 (p = 0.0302) was attenuated after adjustment for BMI (p = 0.187). MC4R rs17782313 did not confer an increased risk for PCOS (p = 0.368) even after adjustments (p = 0.715). Interestingly, the interaction of FTO and MC4R polymorphisms was more significantly associated with PCOS (p = 0.031, adjusted for age and BMI). The FTO variant rs9939609 is associated with Chinese women with PCOS; however, this association is affected by BMI.ConclusionsThe combined pathogenic effect of FTO and MC4R polymorphisms indicates a direct role of the interaction between FTO and MC4R polymorphisms in the development of PCOS.