Three SNPs of UCP-1 including A-3826G, A-1766G, and Ala64Thr (G+1068A) were genotyped among 453 overweight Korean female subjects recruited from an obesity clinic. Four common haplotypes with frequency greater than 0.04 were constructed with three SNPs. For an accurate evaluation of the effects of UCP-1 polymorphism on body fat accumulation, all subjects were tested using computerized tomography to measure the cross-sectional fat tissue areas at abdominal and distal part of the body. By statistical analyses, ht4[GAA] showed a significant association with decreased abdominal fat tissue area (P=0.02, dominant model), fat tissue area at thigh (P=0.008, dominant model), body fat mass (P=0.002, dominant model), and waist-to-hip ratio (P=0.01, dominant model). In addition, ht3[GAG] was associated with the accelerated reduction of waist-to-hip ratio and body fat mass by very low calorie diet among subjects who finished one-month-weight control program (P=0.05-0.006).