AbstractDifferent variant frequencies may lead to different frequencies of the same variants in individuals with drugs resistance and disease susceptibility at the population level. In this study, the allele frequency of three STRs loci including D11S1304, D11S1998, and D11S934 was analyzed on a representative sample of 563 individuals from the capital city of Tehran. The sample included four different ethnic groups. In this sample, 130 individuals were affected with metabolic syndrome (Mets). Calculated parameters on the whole sample were: allele frequency, polymorphic information content values, observed and expected heterozygosity, discrimination power, matching probability, power of discrimination, power of exclusion, and paternity index. For all markers, no significant deviation from Hardy–Weinberg equilibrium was found in observed allele frequencies except D11S1998. There were no significant differences in the allele frequencies in short, medium and long alleles between the metabolic affected subjects and controls. The most significant findings of this study report allele frequency of some STRs on chromosome 11 for the first time in Iran and the observed differences between subjects affected with Mets as opposed to subjects in the control group.