Background Recently, a genome-wide association study identified a strong association between the fat mass- and obesity-associated rs9939609 single nucleotide polymorphism (SNP) and the risk of obesity in European population. However, the results in Chinese population were reported to be contradictory. Therefore, our aim was to examine whether this SNP is associated with obesity and newly diagnosed type 2 diabetes (T2D) in Chinese population. Methods We genotyped rs9939609 in 2587 subjects [obesity 243, overweight 976, normal weight 1368 or newly diagnosed T2D 877, impaired glucose regulation 305, normal glucose tolerance (NGT) 1405] using an allelic discrimination assay-by-design TaqMan method on ABI7900HT. We analysed associations of the rs9939609 SNP with obesity and newly diagnosed T2D through Logistic regression analysis. Results In obesity case control study, we found that the A allele was strongly associated with obesity and overweight. The odds ratios for the allele A versus T were 1.447 for Obesity versus normal weight (95% CI 1.104-1.896, p = 0.007) and 1.363 for Overweight versus normal weight (95% CI 1.149-1.617, p < 0.0001). In T2D case control study, the odds ratios for the allele A versus T were 1.305 for T2D versus NGT (95% CI 1.097-1.552, p = 0.003) and 1.280 for combined T2D and impaired glucose regulation (IGR) versus NGT (95% CI 1.089-1.503, p = 0.003). The associations of the A allele with T2D and combined T2D and IGR remained significant with adjustment for age, sex and body mass index (BMI). Conclusion The fat mass- and obesity-associated gene rs9939609 SNP is strongly associated with risk of obesity and newly diagnosed T2D in the Chinese population. Copyright (C) 2010 John Wiley & Sons, Ltd.