The molybdenum cofactor is essential for the function of sulphite oxidase, xanthine dehydrogenase, and aldehyde oxidase enzymes. Molybdenum cofactor deficiency (MoCD) is a fatal disease resulting in severe neurological damage and death in early childhood. MoCD is an autosomal recessive condition which may mimic ischaemic encephalopathy. Although milder cases with later onset and less severe symptoms have been identified, the classic presentation involves neonatal seizures, progressive encephalopathy and death at an early age. There is currently no effective therapy, and the prognosis is poor. The disorder should be considered in all cases of intractable seizures in the newborn period and infants with clinical and radiological features of ischaemic encephalopathy, especially when no obvious lesion is detected. Blood uric acid measurement should be included in the battery of tests to be performed in all neonates' refractory seizures. We reported here an infant with MoCD who presented with hypoxic ischaemic encephalopathy and identified a novel mutation, c.130C>T in cDNA of the MOCS2 gene from the infant.