Magnetic resonance spectroscopy (MRS) of a 12-year-old female patient with glutaric aciduria type II was compared with data obtained from four healthy age- and sex-matched volunteers. In the clinically active phase, conventional magnetic resonance imaging showed mild ventricular dilatation. Frontal lobe choline/creatine (Cho/Cr) ratio (1.98) was higher than the ratios reported for the comparison participants (1.64 [SD 0.21]). The N-acetylaspartate/creatine (NAA/Cr) ratio (1.95) was lower than normal limits (2.66 [SD 0.23]). After successful riboflavin treatment and dietary restriction for proteins, the NAA/Cr ratio was within the normal range (2.44) and Cho/Cr ratio was below the normal range (1.15), suggesting riboflavin-responsive multiple acyl-coA dehydrogenase deficiency. An elevated Cho/Cr ratio and decreased NAA/Cr ratio is consistent with a demyelinating process in the active phase of glutaric aciduria type II. MRS helps to monitor the progress of the disease and the efficacy of treatment by revealing changes in NAA/Cr and Cho/Cr ratios.