This study was conducted to investigate the effects of Uncoupling protein (UCP) polymorphisms on weight loss. We analyzed associations between polymorphisms of UCP-2, 3 and changes in percentage of obesity phenotypes (Body mass index and percent body fat) after treatment. Materials and Methods: A total of 207 Korean women (BMI over 25) were recruited from the obesity clinic in Kirin Oriental Medical Hospital (Seoul, Korea). All patients were treated with a very low calorie diet and oriental medical therapy for one month. The effect of UCP polymorphisms on changes in obesity-phenotypes were analyzed. For the genotyping of a single nucleotide polymorphism (SNPs), genomic DNA from each subject was extracted from whole blood and genotyped using the TaqMan Method. Associations between changes in percentage of obesity phenotypes (BMI and percent body fat) and UCP polymorphisms were analyzed using age-adjusted general linear model. Results and Conclusions: In this study, AG, GG type of UCP-2 -866A>G, CC, CT type of UCP-2 +4787C>T, CG, GG type of UCP-3 +2564C>G, AG, GG type of UCP-3 +3106A>G, and TC, CC type of UCP-3 +4589T>C played a role as a resistance gene to weight loss.