BACKGROUND: Metabolic syndrome (Met-S) that caused by heredity and Lipoprotein Lipase (LPL). LPL is involved in the metabolism of serum lipids. Variations in LPL alter enzyme activity, and the most common variations are LPL+ 495 T> G and LPL Pvu II C> T. AIM: This study aimed to identify the role of LPL+ 495 T> G and LPL PvuII C> T gene variations in subjects with Met-S in Javanese ethnic based on age stratification. METHODS: We recruited 160 participants of Javanese ethnicity consisting of 80 cases and 80 control subjects. Met-S was diagnosed according to the criteria of NCEP ATP III. Peripheral blood samples were collected to determine biochemical parameters. Screening for both polymorphisms was made by PCR-RFLP. RESULTS: Results found that genotype and allele frequencies for LPL+ 495 T> G were not significantly different between Met-S and controls with and without age stratification. In LPL PvuII C> T based on age stratification, there were significant differences between TT vs CC, recessive and dominant models in Met-S and control. In the age group> 45 years CC genotypes and TC+ CC had increased risk of Met-S compared to TT genotypes. In summary, there was no significant association between LPL+ 495 T> G gene variation with Met-S. CONCLUSION: In LPL PvuII gene variation, TC+ CC is the risk genotype of Met-S in the age group> 45 years.