Aim: To examine the PON1-L55M and-Q192R polymorphisms for polycystic ovary syndrome (PCOS) risk in relation with atherosclerosis risk markers. Methods: Blood samples were collected from 203 women (PCOS [n = 151], control [n = 52]). Genomic DNA was extracted and RFLP method was performed following the amplifications of the target regions. Results: Individuals with 192QR/192RR genotypes had a 2.5-fold increased risk of representing PCOS compared with the individuals with 192QQ genotype. Q192R was more strongly associated with PCOS than previously suggested atherosclerosis risk markers. Q192R status and body mass index values in combination were established to be a significant predictor of PCOS (AUC: 0.655, p = 0.001). Conclusion: This is one of the first studies suggesting the use of combination biomarkers to better predict the risk of developing PCOS.