Hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC) is a rare leukoencephalopathy first described by van der Knaap in 2002. Diffuse cerebral hypomyelination and atrophy of the basal ganglia and cerebellum characterize H-ABC. We report a 9-year-old Japanese boy with H-ABC who had been suspected to have Pelizaeus Merzbacher disease. Brain MRI revealed delayed myelination, however, no other remarkable abnormal laboratory findings were found. PLP1 gene mutation was not detected and he had no nystagmus. He was diagnosed as having H-ABC at the age of 8 years because of supratentorial hypomyelination and progressive atrophy of the basal ganglia and cerebellum on the follow-up MRI. This boy's condition was clinically more severe than those with other reported patients with H-ABC.