Objective: The SLC2A9 gene plays an important role in regulating uric acid reabsorption in renal tubules and increasing the risk of nephrolithiasis. In this study, we sought to investigate the association of SLC2A9 gene polymorphisms with nephrolithiasis risk in Han Chinese from eastern China. Methods: In this case-control study, biochemical variables were evaluated in 328 nephrolithiasis patients and 296 age-matched healthy controls. Three SNPs of SLC2A9 (rs938552, rs1014290 and rs4311316) were genotyped in nephrolithiasis patients and healthy controls using direct sequencing. Results: The genotypic and allelic frequencies of rs938552 was significantly different between nephrolithiasis patients and healthy controls (P value), while rs1014290 and rs4311316 had no association with nephrolithiasis risk. In addition, we found that rs938552 CT and TT genotypes were correlated with a significantly increase nephrolithiasis risk (OR=0.513, 95% CI=0.262–1.004, P<0.01; OR=0.221, 95% CI=0.109–0.450, P<0.01) as compared with the CC genotype in the additive model. Moreover, the nephrolithiasis patients with rs938552 CT and TT genotypes had much higher levels of serum uric acid (P=0.027), 24 hours - urinary calcium (P=0.014) and lower urinary uric acid level as compared with the individuals carrying CC genotype (P=0.038). Conclusion: The rs938552 polymorphism of SLA2C9 gene is closely associated with the risk of nephrolithiasis in Han population in Eastern China. It may affect the stone formation by regulating the metabolism of uric acid and calcium.