A common Single-Nucleotide Polymorphism in the Brain-Derived Neurotrophic Factor (BDNF) gene coding the Val66Met substitution in the pro-BDNF protein has been associated with a number of behavioural and neuroanatomical phenotypes; the latter include, for example, regional differences in volumes of the hippocampus and prefrontal grey matter. Here, we show that the observed regional differences may not stem from a localised effect of this gene. Our analysis of regional brain volume in a cohort of 331 adolescents indicates that the Val66Met substitution has a global effect on brain volume, and that the observed local differences are to be expected if brain allometry-the covariance pattern of regional brain volumes-is taken into account.