The prevalence of overweight and obesity in Chinese school-age population has increased from 5.2% in 1991 to 13.2% in 2006. The growth rate of obesity in this population over the past 5 years has been 160% in urban areas and 400% in rural areas. School-age obesity is associated with the risk of both adult obesity and several obesity-related chronic diseases. Therefore, its prevention is important in public health. Obesity is resulted from interaction of genetic susceptibility and environmental exposures. Genetic susceptibility plays a vital role in increasing the risk of obesity. FTO gene was the first identified gene through GWAS. Several studies have evaluated the associations between some SNPs in FTO gene and risk of obesity and obesity-related traits in both children and CAY10603 adults, but the results remain inconsistent. Although FTO has emerged as a major obesity-related gene particularly in populations of European descent, results in Asian populations are inconclusive. Indeed, no significant association was found between FTO polymorphisms and obesity in Chinese Han population, which was inconsistent with subsequent studies in (20S)-Protopanaxadiol Taiwan and Beijing. In our case-control study, we recruited 1000 Chinese school-age children from northern, central, and southern regions of China. The associations of FTO polymorphisms rs9939609 with the risk of obesity and obesity-related traits were confirmed and the influence of rs9939609 on dietary behaviors was evaluated to in an attempt account for any observed physical and metabolic association. In this case-control study, two novel SNPs were significantly associated with the risk of obesity and obesity-related traits among Chinese school-age children. The inconsistent results may be because of the heterogeneity of the study populations, different definitions of obesity, or the confounding effects of environmental variables. Participants in the present study were school-age children from 7 to 18 years, whereas adult women aged from 50 to 70 years were included in another study. In a European population, Loos et al. found that the association between FTO and obesity was more significant in children than in adults.