We report a newborn with exaggerated startle reactions and stiffness of neonatal onset, the prototypical signs of hyperekplexia. Startle and flexor spasms, leading to apnoea, did not respond to treatment with clonazepam but did partially to sodium valproate. Molecular analysis of GLRA1 revealed no mutations. The incidental finding of hypouricemia led to a work-up for molybdenum cofactor (MoCo) deficiency; the diagnosis was confirmed by the altered urine chemistries, including elevated urine S-sulphocysteine. Despite persistence of the spasms, clinical or electrographic seizures were never detected before the infant died at age 1 month. In this patient, the concurrence of hyperekplexia and MoCo deficiency was suggestive of impaired gephyrin function. GPH mutational analysis, however, showed no abnormalities. The patient was eventually found to harbour a novel c.1064T > C mutation in exon 8 of the MOCS1 gene. Despite extensive sequence analysis of the gene, the second causative mutation of this recessive trait still awaits identification. MoCo deficiency should be considered in the differential diagnosis of neonatal hyperekplexia, particularly in the instances of refractoriness to clonazepam, an early demise in infancy or the evidence of no mutations in the GLRA1 gene.