The relation of -55C/T polymorphism of uncoupling protein 3 (UCP3) with metabolic syndrome (MS) has been evaluated only in one previous study with contradictory results. The aim of our study was to investigate the association of -55C/T polymorphism of UCP3 gene with MS. A population of 817 obese Caucasian patients was analyzed in a cross-sectional survey. Genotype of UCP3 gene -55C/T was studied. To estimate the prevalence of MS , the definitions of the ATPIII were considered. Five hundred and ninety-four patients (72.7%) had the genotype -55CC (wild group), whereas 223 patients (27.3%) had the genotype -55C/T. Genotype -5TT was not detected. Prevalence of mutant UCP genotypes was similar in patients with MS (75.7% wild genotype and 24.3% mutant genotype) and without MS (69.7% wild genotype and 30.3% mutant genotype). Odds ratio of MS wild vs. mutant genotype was 1.17 CI 95%: 0.99-1.38). Total cholesterol and low density lipoprotein (LDL) cholesterol concentrations were lower in mutant-type group than wild-type group in patients with MS. No differences in other parameters were detected between genotypes in the same group of MS. -55C/T UCP polymorphism is not major risk factor for the MS. However, in mutant group of -55CC UCP3 gene in patients with MS, total cholesterol and LDL cholesterol were lower than wild-type patients.