Objective To investigate the relationship between glucokinase regulator protein ( GCKR) gene polymorphism rs780094 and hyperuricemia in Uygur in Xinjiang. Methods A case-control study including 1 026 patients with hyperuricemia and 1 030 normal subjects was conducted. All the subjects were genotyped for GCKR gene rs780094 by Sequenom MassARRAY system. The results of rs780094 genotype and allele frequency between hyperuricemia group and control group were compared. The associations of different genotypes of rs780094 with blood pressure, blood lipid, and blood glucose were analyzed. Logistic regression analysis was used to analyse the relationship between polymorphism of rs780094 and hyperuricemia in Uygur in Xinjiang. Results The distributions of three genotypes(G/G, A/G, A/A) and two allele frequency (G and A) in GCKR rs780094 revealed statistical difference ( P<0. 05 ) between hyperuricemia group and control group. A tendency toward association with hyperuricemia was observed under dominant model(OR=1. 295, 95%CI 1. 078~1. 554,P=0. 006) and recessive model(OR=1. 284, 95% CI 1. 024 ~1. 611,P=0. 030). The levels of systolic blood pressure, diastolic blood pressure, and total cholesterol were lower in hyperuricemia group with GCKR gene rs780094 loci GG genotype than those with AA+AG genotype. After adjusting confounding factors which had significant difference in the single factor analysis, logistic regression analysis showed that rs780094 A/A and A/G might be risk factors of hyperuricemia in Uygur in Xinjiang (OR=1. 355,95% CI 1. 094 ~1. 679,P=0. 005). Conclusion The GCKR rs780094 is associated with hyperuricemia in Uygur in Xinjiang. The A/A and A/G genotype of the GCKR rs780094 may increase the risk of hyperuricemia.