Background: Variation in drug resistance and susceptibility to various diseases may be related to difference in allele frequencies of the variants at the population level.

Objectives: The present study aimed to investigate the allele frequencies of five short tandem repeats (STR) loci in two different chromosomes of candidates from Tehran Lipid and Glucose Study.

Materials and Methods: For this study, a representative sample of 563 individuals (130 affected by metabolic syndrome) from Tehran, including four different ethnic groups of Iran, was selected. Five STRs including D12S1632, D12S329, D12S96, D16S3096 and D16S2624 were analyzed using the fragment analysis method. Allele frequency, polymorphism information content (PIC) values, observed and expected heterozygosity, discrimination power, matching probability, power of discrimination, power of exclusion and paternity index were calculated for the whole sample.

Results: There was no significant deviation in allelic frequencies from Hardy-Weinberg equilibrium for all the studied markers except for D12S1632 and D12S329. The long alleles in D12S329 were significantly more frequent in patients with metabolic syndrome (P < 0.05).

Conclusions: This study revealed allele frequency of some STRs on chromosome 12 and 16 for the first time in Iran, and indicated differences between subjects with metabolic syndrome and subjects in the control group.