We report a male case of 3-hydroxyisobutyric aciduria (3HiB-uria) with severe brain damage. He had mild asphyxia at birth. He needed tube feeding for a month. He showed mild dysmorphic features, including low set ears, a long philtrum and micrognathia. At 4 months of age he had acute encephalopathy. Thereafter, severe brain damage remained and mechanical ventilation care was needed all day. After he had been admitted to our hospital at 3 years of age, repeated organic acid analysis of urine confirmed the diagnosis of 3HiB-uria. This patient had been previously diagnosed as having cerebral palsy and sequelae of acute encephalopathy.