The association of a 45-bp insertion/deletion (UCP2-45 bp I/D) polymorphism in uncoupling protein 2 with body mass index (BMI) remains controversial. A case-control study was conducted to examine the association in a Chinese population. The 1,526 subjects recruited in downtown Beijing and genotyped included 616 obese subjects with BMI >28 and 910 age- and gender-matched controls with BMI <24. The association of the polymorphisms with obesity was estimated using multivariate logistic regression in three models of inheritance. The odds ratios were 1.08 (95 % CI 0.846-1.368; P = 0.551) in the dominant model, 0.931 (0.751-1.154; P = 0.513) in the additive model, and 1.18 (0.550-2.550; P = 0.666) in the recessive model. The overall comparison of the genotype distributions in obese and control subjects using the chi-square test yielded P = 0.801. Our study demonstrated no association between UCP2-45 bp I/D and BMI variation in the Chinese population.