Background: Variants on the FTO gene increase obesity risk. FTO has been previously associated with alterations in brain structure, but less is known about the influence of FTO on brain structure in children. Methods: We examined differences in grey matter volume (GMV) and cortical thickness (CT) between FTO SNP rs9939609 allele carriers in 2 to 15 year old children. Structural MRI data were drawn from a longitudinal study of healthy brain development (Resonance). We cross-sectionally analyzed differences in GMV and CT in typically developing children grouped by FTO risk alleles: AA high risk, n = 53, age = 7.4 ± 2.9 y, 26M,27F, BMIz = 0.32 ± 1.13; AT moderate risk, n = 142, age = 7.31 ± 2.98 y, 77M,65F, BMIz = 0.25 ± 1.21; TT low risk, n = 89, age = 7.26 ± 3.1 y, 56M,33F, BMIz = -0.0035 ± 1.38. GMV and CT measurements were obtained using FreeSurfer. Preliminary multivariate GLM analysis was performed in SPSS to assess group differences (Bonferroni corrected for multiple comparisons, P < 0.05), where GMV and CT were adjusted for age, sex and BMIz, with additional total intracranial volume adjustments for GMV. Results: The AT vs. TT group demonstrated alterations in left amygdala, right cerebellum, left superior temporal sulcus and left fusiform gyrus (lower GMV); right superior parietal cortex (higher CT). The AA vs. TT group showed alterations in left caudal anterior cingulate cortex and right cerebellum (lower GMV), right frontal pole (higher GMV+CT), and left lateral occipital cortex (higher CT). Conclusions: Structural brain alterations associated with FTO risk alleles could predict future obesity. Future longitudinal analyses will examine effects of FTO variants on brain development and weight trajectories, with potential implications for neurobehaviorally targeted obesity prevention.