Aims SLC2A9 is also known as glucose transporter9 (GLUT9) or urate efflux transporter (URAT)v1, which should be involved in the transport of glucose and uric acid. To further verify it, the correlation of the SLC2A9 polymorphisms(rs13129697,rs7442295) with T2DM, Hyperuricemia (HUA) and T2DM compared with HUA will be investigated in male Han Chinese. Methods Two SNPs of the SLC2A9, rs13129697, rs7442295, were genotyped in 285 T2DM patients, 300 HUA patients and 198 T2DM compared with HUA patients respectively through TaqMan-MGB Duplex real-time PCR, and 550 healthy subjects were selected as control group. The total 1333 subjects were all recruited from the Affiliated Hospital of Qingdao University Medical School. Results Compared with control group, the variant SNP of rs13129697 was both significantly associated with HUA group(P<0.001) and T2DM complicated HUA group(P<0.05), but not with pure T2DM group. After adjustment for age, triglyceride and cholesterol, logistic regression analysis showed that people with GT、GG genotype had lower risks of HUA(OR=0.615,95%CI: 0.432-0.877,P=0.007;OR=0.447, 95%CI:0.271-0.736, P=0.002)and T2DM complicated HUA(OR=0.578,95%CI: 0.360-0.923, P=0.022;OR=0.393,95%CI: 0.208-0.740,P= 0.004) than people with TTgenotype. However, there were no statistical significance between control group and T2DM group, HUA group, or T2DM complicated with HUA group in rs7442295 genotypes(P>0.05). Conclusion The rs13129697 polymorphism of the SLC2A9 gene, but not rs7442295 is associated with impaired glucose tolerance/impaired fasting glucose complicated with hyperuricaemia. And G allele may protect against the risk to develop HUA.