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To examine the impact of single nucleotide polymorphisms(SNPs)in obesity-related genes on the incidence and durative of obesity in childhood and adolescence.Based on the Beijing Child and Adolescent Metabolic Syndrome (BCAMS) Study, 780 school children aged 6 to 16 years were followed-up in 2010, and assessed for body size parameters. Venipuncture blood samples were collected after a 12-hour overnight fast. Genomic DNA was isolated from peripheral blood white cells under the salt fractionation method. SNPs were genotyped by ABI 5700 real time PCR(FTO rs9939609)and TaqMan Allelic Discrimination Assays with the GeneAmp 7900 Sequence Detection System(Applied Biosystems,Foster City, CA, USA) (FTO rs6499640, FAIM2 rs7138803,NPC1 rs1805081, MC4R rs17782313, BDNF rs6265, GNPDA2 rs10938397). Both overweight and obesity were diagnosed by the Chinese age- and sex- specific body mass index(BMI) cutoffs. Two independent sample t-test, Chi-square test and multiple logistic regression analysis were performed.During the 6 years follow-up period, the incidence of obesity in the total sample 8.5%, and 65.1% individuals had persisted their obese status. The genotypes of the SNPs except BDNF rs6265 were in Hardy-Weinberg equilibrium in each group (P0.05). The incidence rates of obesity increased with FTO rs9939609 TT,TA and AA genotypes(χ(2) for trend = 8.030, P0.05). In the non-obese sub-cohort, after adjusted for sex, age at the initial time of follow up and residential area, when compared with children carrying FTO rs9939609 T-allele, a significantly relative risk of obesity was observed for children carrying the rs9939609 A-allele(OR = 2.42, 95%CI:1.31-4.47, P = 0.005). In the obese sub-cohort, FTO rs9939609 A-allele was significantly associated with durative of obesity (OR = 1.72, 95%CI:1.07-2.77, P = 0.026). However, no statistical significant associations were seen between other SNPs(FTO rs6499640, FAIM2 rs7138803, NPC1 rs1805081, MC4R rs17782313, GNPDA2 rs10938397)and the incidence or durative of obesity(all P0.05). The genetic risk score was associated with the risk of occurrence of obesity(OR = 16.42, 95% CI:3.59-75.10, P0.001) after adjusted for residential area, sex, age at the initial time of follow up and baseline BMI.We confirmed the association of FTO rs9939609 with incidence and durative of obesity in children. Early intervention was recommended on the high risk individuals who carrying more risk alleles in obesity-related genes.