Recent reports suggested functional abnormalities of the brain stem in autistic children. Moreover, structural brain abnormalities have also been reported, so we analyzed magnetic resonance imaging (MRI) scan in autistic children. MRI scans for 29 autistic children were compared with 15 control MRI scans. The midbrain and pons were measured. The midbrain and pons size were found to be significantly smaller in the autistic group. This suggests that the structure of the brain stem is anatomically altered in autistic children.