Sirtuin 1 (SIRT1) is a longevity gene that protects cells against oxidative and genotoxic stress. This study aimed to investigate the associations of SIRT1 gene single nucleotide polymorphisms (SNPs), rs7895833, rs7069102, and rs2273773, with various laboratory data in 1279 Japanese health checkup examinees. The genotyping was performed using a polymerase chain reaction (PCR) with confronting 2-pair primers (CTPP) assay. Concerning rs7895833 (A allele frequency: 0.290), body fat ratio and body mass index were high in the AA carriers of male subjects, and diastolic blood pressure was high in the AA carriers of female subjects. Concerning rs7069102 (G allele frequency: 0.181), body fat ratio and systolic blood pressure were high in the GG carriers of male subjects. Concerning rs2273773 (C allele frequency: 0.323), fasting glucose and body fat ratio were high in the TT carriers of male subjects, and systolic and diastolic blood pressures were high in the CC carriers of male subjects. Thus, the A allele of rs7895833, G allele of rs7069102, and T allele of rs2273773 carried a high risk for obesity in men. Furthermore, the A allele of rs7895833 in women, and the G allele of rs7069102 and C allele of rs2273773 in men, carried a high risk for hypertension. The T allele of rs2273773 in men carried a high risk for hyperglycemia. In conclusion, these SIRT1 gene polymorphisms are associated with high body fat and blood pressure in Japanese, especially in men. The allele frequencies of rs7895833 and rs7069102, which are different from Caucasians, might explain why Japanese show less marked obesity compared with Caucasians.