Calcium oxalate (CaOx) nephrolithiasis has a complex pathogenic mechanism. Besides environmental factors, genetic factors also have influence on stone formation. This study represents the effects of heparan sulfate (HSPG2) gene polymorphism for determining the risk of urolithiasis. We investigated 143 CaOx stone formers with 158 healthy individuals for the BamHI restriction site polymorphism located in intron 6 of the HSPG gene using the polymerase chain reaction, restriction fragments length polymorphism method. After digestion with BamHI, the polymorphism was assumed to cause three genotypes according to the banding types as GG (242 bp), GT (242, 144, and 98 bp) and TT (144 and 98 bp). According to the genotype frequencies between the groups, TT genotype showed significantly increased risk for urolithiasis than TG and GG genotypes. We concluded that HSPG2 gene polymorphism might be one of the genetic factors affecting the CaOx stone formation.