Objective To assess the density difference in the cerebral grey and white matter in children with autistic disorder. Methods Voxel based morphometry (VBM) in conjunction with statistical parametric mapping was applied to the structural magnetic resonance images of 17 autistic disorder children and 15 normal controls. Results Compared with the controls, the grey matter density in autistic disorder children had significant decrease in the fight anterior lobe of cerebellum and increase in the bilateral inferior parietal lobule, right supramarginsl gyrus, right postcentral gyrus, right posterior lobe of cerebellum, right superior temporal gyms, left precunens and left cuneus (P<0.001). Significant dusters of reduced white matter density were found in the region of right anterior cingulated and right medial frontal gyms (P< 0.001) in autistic disorder children in comparison with controls. Conclusion The findings indicate structural grey and whim matter are significantly abnormal in children with autistic disorder and the deficits are widespread in brain regions.