To elucidate the potential impact of the variants of the UCP2 gene on obesity phenotypes, we have genotyped four polymorphisms in UCP2 among 988 Korean subjects using TaqMan methods, and three common haplotypes with frequency greater than 0.1 were constructed in the Korean population. No significant associations were detected with the risk of metabolic syndrome by logistic regression analyses. However, the 45 base-pair ins/del polymorphism (+3474 ins/del) in the 3' untranslated region (3' UTR) showed significant association with body mass index (P=0.007, P(corr)=0.02) and waist circumference (P=0.005). Further subgroup analysis revealed that the genetic effects were more apparent among female subjects. In addition, a summary of the controversial genetic effects on obesity mediated by UCP2 polymorphisms from previous studies is also given. Our results suggest that subjects with a 45bp insertion allele of UCP2+3474 ins/del might have a higher risk of developing obesity, although the biological effects of this variant are not completely known.