We studied the in vivo cerebral metabolites and documented the presence of MECP2 gene mutations in six Chinese females with Rett syndrome. Magnetic resonance spectroscopy spectra from the frontal lobe (gray and white matter) and deep gray nuclei (basal ganglia and thalamus) of either side were obtained. N-acetylaspartate/total creatine, choline/total creatine, and N-acetylaspartate/choline ratios were analyzed and compared with six healthy age-matched female control subjects. MECP2 gene mutation was identified in four patients; one patient had polymorphism and one patient did not have gene mutation. N-acetylaspartate/total creatine of the frontal lobe of all patients (mean: 2.63, S.D. = 0.33) was decreased compared with age-matched control subjects (mean: 3.15, S.D. = 0.27), and the difference was statistically significant (P = 0.017) with a mean difference of 0.52 (95% CI = 0.68-0.36). The difference in all other metabolite ratios in the frontal lobe and deep gray nuclei were not statistically significant compared with age-matched control subjects. Mild frontal lobe and anterior temporal lobe atrophy was present in three patients. Proton-magnetic resonance spectroscopy is a sensitive method capable of detecting the biochemical changes in Rett syndrome and is able to detect changes before conventional magnetic resonance imaging. Our preliminary results suggest that reduction in N-acetylaspartate/total creatine ratio may not be related to the MECP2 mutation.