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Uncoupling protein 2 (UCP2) is a member of the mitochondrial transporter superfamily. It is proposed as a candidate gene for obesity. A common G/A polymorphism in the promoter region of this gene is associated with enhanced adipose tissue mRNA expression in vivo. Using a PCR-RFLP method, we genotyped the UCP2 –866G/A polymorphism in 75 unrelated nonobese nondiabetic Iranians. The frequencies of the UCP2 –866G/A genotypes in 75 Iranian normal subjects were 7 (9.4%) for AA, 41 (54.6%) for GA, and 27 (36%) for GG. Significantly higher HDL cholesterol was detected in people with the GG genotype ( p = 0.02) compared to individuals with the GA and AA genotypes. The frequency distribution results were compared with data from Japanese, Italians, Germans, Austrians, and Danes. Our allele frequencies were significantly different from the Japanese data from two different reports (P < 0.025) but not from the others. The Japanese data showed a higher frequency of the AA genotype, which is associated with a low prevalence of obesity, than the Caucasian individuals’ data did. In conclusion, a single nucleotide polymorphism in the promoter region of the UCP2 gene has a significant association with HDL cholesterol level in Iranian nonobese nondiabetic subjects. Also, our allele-frequency distribution for this single nucleotide polymorphism is closer to European Caucasians than to Japanese in nonobese nondiabetic individuals.