Background/Aims: KLOTHO, a type-1 transmembrane protein with glucurodinase activity, is expressed in tissues responsible for calcium homeostasis such as the kidney, parathyroid gland and the epithelium of the choroid plexus in the brain. Given the emerging evidence indicating a novel regulatory function for KLOTHO protein in renal calcium and phosphate homeostasis, the present study aims to investigate the association between KLOTHO genetic polymorphisms and kidney stone (KS). Methods:KLOTHO gene polymorphisms G395A in the promoter region, F252V in exon 2, and C1818T in exon 4 were investigated in 108 patients with renal calcium stone formation and 51 age-matched healthy volunteers with no history of renal stone formation, using polymerase chain reaction. Results: GG genotype of G395A KLOTHO polymorphism had approximately 2-fold increased KS risk compared with the homozygous genotype AA and heterozygote GA (OR 1.849, 95% CI 1.016–3.364, p = 0.044). We also found that non-A allele carriers had significantly higher KS risk associated with the KS clinical characteristics including hypercalcemia, hypophosphatemia and phosphaturia. Conclusion: Our findings suggested that the G395A polymorphism of KLOTHO gene is associated with the KSs and may act as a risk factor for the development of KS disease.