Background and purposeAlternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disease caused by ATP1A3 mutations. Using voxel‐based morphometry (VBM) analysis, we compared an AHC patient cohort with controls. Additionally, with single‐case VBM analysis, we assessed the associations between clinical severity and brain volume in patients with AHC.Materials and methodsTo investigate structural brain changes in gray matter (GM) and white matter (WM) volumes between 9 patients with AHC and 20 age‐matched controls, VBM analysis was performed using three‐dimensional T1‐weighted magnetic resonance imaging. Single‐case VBM analysis was also performed on nine patients with AHC to investigate the associations between the respective volumes of GM/WM differences and the motor level, cognitive level, and status epilepticus severity in patients with AHC.ResultsCompared with controls, patients with AHC showed significant GM volume reductions in both hippocampi and diffuse cerebellum, and there were WM reductions in both cerebral hemispheres. In patients with AHC, cases with more motor dysfunction, the less GM/WM volume of cerebellum was shown. Three of the six cases with cognitive dysfunction showed a clear GM volume reduction in the insulae. Five of the six cases with status epilepticus showed the GM volume reduction in hippocampi. One case had severe status epilepticus without motor dysfunction and showed no cerebellar atrophy.ConclusionWith single‐case VBM analysis, we could show the association between region‐specific changes in brain volume and the severity of various clinical symptoms even in a small sample of subjects.