The X-linked monoamine oxidase A (MAO A) gene, coding for an enzyme especially involved in the serotonin catabolism, presents a well-characterized functional polymorphism (long and short variants) in the promoter region that alters the transcriptional activity of the gene and hence the function of the corresponding proteins. Using optimized voxel-based morphometry, we studied the effect of this functional polymorphism on brain morphology in normal individuals. Fifty-nine male healthy individuals (33 MAO A-high and 26 MAO A-low) were investigated. Voxel-based morphometry showed that the carriers of the long variant were significantly associated with loss of grey matter in orbitofrontal cortex, bilaterally. This study reveals pronounced genotype-related structural changes in a specific prefrontal region previously observed to mediate neurofunctional responses in behavioral tasks.