Five patients with Prader-Willi syndrome underwent magnetic resonance imaging and proton magnetic resonance spectroscopy. Magnetic resonance images revealed mild abnormalities, including slight ventriculomegaly, cortical atrophy, and a small brainstem, in all cases. The N-acetylaspartate/Choline (NAA/Cho) and N-acetylaspartate/Creatine (NAA/Cr) ratios were decreased in one (Case 1) and two (Cases 1 and 4) patients, respectively. The Choline/Creatine (Cho/Cr) ratio did not differ from those in control subjects. Thus, in patients with Prader-Willi syndrome, it is thought that there may be neuron loss or a neuron dysfunction caused by a chromosome abnormality. Statistically significant relationships were observed between IQ (DQ) and the NAA/Cho and Cho/Cr ratios: r = 0.895 (P < .05, NAA/Cho ratio) and r = -0.898 (P < .05, Cho/Cr ratio). This suggests that the parietal lobe pathology detected on 1H-magnetic resonance spectroscopy may be associated with more global brain damage and with loss of cognitive functions.