Background: Various twin studies revealed that the influence of genetic factors on psychological diseases or behaviour is more expressed in socioeconomically advantaged environments. Other studies predominantly show an inverse association between socioeconomic status (SES) and childhood obesity in Western developed countries. The aim of this study is to investigate whether the fat mass and obesity-associated (FTO) gene interacts with the SES on childhood obesity in a subsample (N=4406) of the IDEFICS (Identification and prevention of Dietary- and lifestyle-induced health EFfects In Children and infantS) cohort. Methods: A structural equation model (SEM) is applied with the latent constructs obesity, dietary intakes, physical activity and fitness habits, and parental SES to estimate the main effects of the latter three variables and a FTO polymorphism on childhood obesity. Further, a multiple group SEM is used to explore whether an interaction effect exists between the single nucleotide polymorphism rs9939609 within the FTO gene and SES. Results: Significant main effects are shown for physical activity and fitness (standardised β s = -0.113), SES (β s = -0.057) and the FTO homozygous AA risk genotype (β s = -0.177). The explained variance of obesity is ∼9%. According to the multiple group approach of SEM, we see an interaction between SES and FTO with respect to their effect on childhood obesity (Δχ 2 =7.3, df=2, P=0.03). Conclusion: Children carrying the protective FTO genotype TT seem to be more protected by a favourable social environment regarding the development of obesity than children carrying the AT or AA genotype.