Background: We investigated structural brain morphology of intellectually disabled children with Williams (WS) syndrome and its relationship to the behavioural phenotype. Methods: We compared the neuroanatomy of 15 children (mean age:13±2) with WS and 15 age/gender-matched healthy children using a manual region-of-interest analysis to measure bulk (white+grey) tissue volumes and unbiased fully-automated voxel-based morphometry to assess differences in grey/white matter throughout the brain. Ratings of abnormal behaviours were correlated with brain structure. Results: Compared to controls, the brains of children with WS had a decreased volume of the right parieto-occipital regions and basal ganglia. We identified reductions of grey matter of the parieto-occipital regions, left putamen/globus pallidus and thalamus; and in white matter of the basal ganglia and right posterior cingulate gyrus. In contrast, significant increases of grey matter were identified in the frontal lobes, anterior cingulate gyrus, left temporal lobe, and of white matter bilaterally in the anterior cingulate. Inattention in WS was correlated with volumetric differences in the frontal lobes, caudate nucleus and cerebellum, and hyperactivity was related to differences in the left temporal and parietal lobes and cerebellum. Finally, ratings of peer problems were related to differences in the temporal lobes, right basal ganglia and frontal lobe. Conclusions: In one of the first studies of brain structure in intellectually disabled children with WS using voxel-based morphometry, our findings suggest that this group has specific differences in grey/white matter morphology. In addition, it was found that structural differences were correlated to ratings of inattention, hyperactivity and peer problems in children with WS.