We report MRI and proton MR spectroscopy (MRS) findings in a 12-month-old girl with Epstein-Barr virus encephalitis. CT and MRI showed focal lesions in the basal ganglia. MRS of the lesions showed decreased N-acetyl aspartate and elevation of some amino acids, indicating an infectious rather than ischemic etiology. This case illustrates the use of MRS to narrow differential diagnosis.