Objective To clarify the contradictory findings in patients with obesity and type 2 diabetes by meta-analysis. Methods PubMed and Embase were searched for articles published up to March 2009. All studies on the association of FTO polymorphisms with obesity and type 2 diabetes were included. Pooled odds ratio was calculated using the model of fixed or random effects. Sensitivity analysis was performed to evaluate the stability of meta-analytic results. Results Meta-analysis suggested that rs9939609 A allele was more significantly associated with obesity risk than T allele(3 studies /2 004 cases and 4 544 control subjects):random effect odds ratio(OR) =1.28,95%CI=1.05 and 1.55,P heterogeneity =0.05,I 2 =66.6%. Similar results were observed in rs8050136 polymorphism(3 studies/2 404 cases and 5 713 control subjects) :fixed effect OR =1.25,95%CI=1.13, 1.37,P heterogeneity=0.12,I 2 =51.9%. However,no significant association was found between genetics and risk of type 2 diabetes after control of potential confounders(at least for BMI) either for rs9939609(fixed effect OR=1.05,95% CI=0.97,1.13) or for rs8050136 polymorphism(fixed effect OR =1.07,95%CI:0.99,1.16) . Furthermore,the sensitivity analysis strengthened our confidence in validity of the association. Conclusion FTO polymorphisms are associated with obesity but not with type 2 diabetes in East Asian populations. Further large-scale studies are required to conclusively establish the association. Objective To clarify the contradictory findings in patients with obesity and type 2 diabetes by meta-analysis. Methods PubMed and Embase were searched for articles published up to March 2009. All studies on the association of FTO polymorphisms with obesity and type 2 diabetes were included. Pooled odds ratio was calculated using the model of fixed or random effects. Sensitivity analysis was performed to evaluate the stability of meta-analytic results. Results Meta-analysis suggested that rs9939609 A allele was more significantly associated with obesity risk than T allele (3 studies / 2 004 cases and 4 544 control subjects): random effect odds ratio (OR) = 1.28, 95% CI = 1.05 and 1.55, P heterogeneity = 0.05, I2 = 66.6%. Similar results were observed in rs8050136 polymorphism / 2 404 cases and 5 713 control subjects): fixed effect OR = 1.25, 95% CI = 1.13, 1.37, P heterogeneity = 0.12, I2 = 51.9%. However, no significant association was found between genetics and risk of type 2 diabetes after control of potential confounders (at least for BMI) either for rs9939609 (fixed effect OR = 1.05, 95% CI = 0.97,1.13) or for rs8050136 polymorphism (fixed effect OR = 1.07, 95% CI: 0.99, sensitivity analysis strengthened our confidence in validity of the association. Conclusion FTO polymorphisms are associated with obesity but not with type 2 diabetes in East Asian populations. Further large-scale studies are required to conclusively establish the association.