The oxysterol hypothesis of cholesterol homeostasis states that oxysterol mediates feedback regulation of cholesterol biosynthesis. Oxysterol-binding proteins have been implicated in the control of lipid synthesis and metabolism. In a genome-wide case-control association study in Japanese individuals, we found that the three single-nucleotide polymorphisms (SNPs) with the smallest P-values were located in the fifth intronic region of the oxysterol-binding protein-like 10 (OSBPL10) gene. In this study, we examined the association between polymorphisms in the OSBPL10 gene and risk factors for the metabolic syndrome in the Tanno and Sobetsu Study. We selected four SNPs, including three non-coding SNPs in intron 5 and a coding SNP (D254N) in exon 6. Genotype frequencies of the polymorphisms satisfied the conditions for Hardy-Weinberg equilibrium. We found that the low-density lipoprotein (LDL) cholesterol of individuals with the rs2290532 (D254N) polymorphism was significantly greater in subjects with the CC+CT genotype than in subjects with the TT genotype (124.3+/-1.3 vs. 111.6+/-4.1 mg per 100 ml, P=0.009). However, there were no significant differences in systolic or diastolic blood pressure, high-density lipoprotein cholesterol or triglyceride levels. Multiple regression analysis showed that rs2290532 (D254N) was associated with LDL cholesterol independent of age, sex or body mass index. Comparison of the genotype frequency in both groups indicated that the genotype associated with low risk (TT) reduced the risk of hyper-LDL cholesterolemia significantly (P=0.003), with an odds ratio of 0.35 (95% confidence interval=0.17-0.76). Overall, the rs2290532 (D254N) polymorphism in OSBPL10 may predispose individuals with this SNP to hyper-LDL cholesterolemia.