A 20-day-old infant with molybdenum cofactor deficiency, a rare encephalopathy, was investigated using cerebral MRI and proton MR spectroscopy. Images demonstrated extensive white-matter destruction with large cavities. The short-echo-time MR spectrum acquired in the parieto-occipital area was characterised by global loss of signal and accumulation of lactate. No additional signal in relation to the pathophysiology of the disease was detected. The brain metabolic abnormalities observed in this patient may reflect destruction of white matter and the presence of large cavities.