Isolated sulphite oxidase deficiency (ISOD) is a rare autosomal recessive inborn error of metabolism, which may present at birth with intractable seizures (often of prenatal onset) and severe neurological abnormalities. In infants who survive, lens dislocation may occur from 8 weeks of age. The neuropathological findings in ISOD are similar to those seen in severe perinatal asphyxia. We describe two siblings with ISOD born to healthy non-consanguineous parents. The first child presented within 48 h of birth with poor feeding and seizures. He died from septicaemia on day 20 of life. The clinical presentation, neuroradiology and autopsy suggested a diagnosis of severe hypoxic ischaemic encephalopathy with a low recurrence risk. The second child presented with seizures within an hour of birth. She lived for 16 months during which time she failed to make developmental progress and continued to experience intractable seizures. Her neuroradiology was similar to her brother’s. A diagnosis of ISOD was suggested from high urinary S-sulphocysteine in the second child and confirmed by the absence of sulphite oxidase activity in skin fibroblast culture. The diagnosis has enabled the couple to access prenatal testing in a subsequent pregnancy. Conclusion:Isolated sulphite oxidase deficiency is an autosomal recessive condition which may mimic ischaemic encephalophathy. The disorder should be considered in all cases of intrauterine seizures, intractable seizures in the newborn period and infants with clinical and radiological features of ischaemic encephalophathy, especially when no obvious insult can be determined.