Isolated sulphite oxidase deficiency (ISOD) is a very rare hereditary metabolic disorder. Imaging findings of the neonatal form of ISOD, including multicystic leukoencephalopathy with brain atrophy, resemble those of severe ischemic changes of the brain. We report the case of a ten-month-old boy who exhibited neonatal seizures on the 24th day after birth. Excessive quantities of sulphite and S-sulphocysteine in the urine and normal blood uric acid were noted. These findings were consistent with those of ISOD. Point mutations were found in two alleles of the sulphite oxidase (SUOX) gene. One of the mutations was a 1029 C > G mutation, which resulted in an amino acid substitution of tyrosine to a stop code (Y343 X); and the other was a 479 G > A mutation, which resulted in an amino acid substitution of arginine to glutamine (R160 Q). Y343 X is a novel SUOX gene mutation. A review of the literature, including data from this report, showed that 3 of 6 cases had typical imaging findings characterized by initial cerebral edema followed by dramatic multicystic leukoencephalopathy. We emphasize that neonatal ISOD should be included in the differential diagnosis of neonates with unexplained hypoxic-ischemic changes on neuroimaging studies.