PURPOSE: We investigated polymorphisms of the osteopontin (OPN) gene to explore whether they could be used as a gene marker for determining the risk of urinary calcium stones. MATERIALS AND METHODS: A total of 76 patients with urinary calcium stones and 124 controls were studied. Two single nucleotide polymorphisms with nonsynonymous amino acid located at positions 9,402 (Arg/His) and 9,171 (Asn/Ser) in the OPN gene were genotyped using the TaqMan 5' nuclease assay in a PRISM 7700 sequence detection system. Results were analyzed with Fisher's exact test. RESULTS: Results revealed a significant different polymorphism at OPN gene position 9,402 between patients with urinary calcium stones and control subjects. The frequency of the A/G genotype at position 9,402 in patients with urinary calcium stones was significantly higher than that in control subjects (p <0.01). The frequency of the A allele at position 9,402 was significantly higher in the patient than in the control group (4.6% vs 0.4%, p <0.01). There was no statistical difference in this polymorphism at OPN gene position 9,402 between genotype distribution and clinical characteristics associated with urinary calcium stones. There was no difference in the polymorphism at OPN gene position 9,171 between the patient and control groups. CONCLUSIONS: Polymorphism at position 9,402 of the OPN gene is highly associated with urinary calcium stones and it is a candidate genetic marker for evaluating the genetic risk of urinary calcium stone disease, whereas polymorphism at position 9,171 of the OPN gene is not associated with urinary calcium stone disease.