Objective:To explore the correlation of the glucokinase regulatory protein(GCKR) gene rs3817588 and rs780094 single nucleotide polymorphisms(SNPs) with polycystic ovary syndrome(PCOS) and its related metabolic indices in Chongqing Han popu-lation. Methods:Totally 147 patients with PCOS and 156 normal controls were recruited and genotyped by TaqMan SNP genotyp-ing assay;Hyperinsulinemic-euglycemic clamp was performed on all patients and 20 controls. Results:Nither statistical differences in genotype and allele frequencies of rs3817588(OR=0.929,95%CI=0.541 to 1.594, ?字2=0.72,P=0.79;OR=0.995,95%CI=0.759 to 1.304,?字2=0.00,P=0.97,respectively),nor statistical differences,in genotype and allele frequencies of rs780094(OR=1.427,95%CI=0.974 to 1.598, ?字2=2.74,P=0.10;OR=0.880,95%CI=0.700 to 1.107, ?字2=1.20,P=0.27,respectively) was found between the two groups. Conclusion:GCKR gene rs3817588 and rs780094 polymorphisms have no association with PCOS or its related metabolic factors in Han population in Chongqing.