In vivo proton and phosphorus magnetic resonance spectroscopy (MRS) studies were performed at 1.5 T on two patients (siblings) diagnosed as having a mitochondrial cytopathy. The clinical diagnosis was based on a complete battery of biochemical tests, electron microscopy and modified Gomori trichrome stain studies of muscle. Proton spectra from the gastrocnemius muscle were recorded using the stimulated echo acquisition mode (STEAM) and the phosphorus spectra were obtained using the depth-resolved surface coil spectroscopy (DRESS) sequence. Proton resonances from neutral fats in the patients were found to be strikingly weak compared to normals. The ratios [PCr]/[ATP] and [PCr]/[Pi] and the pH values, as inferred from the phosphorus MRS, were found to be marginally decreased compared to normals. These studies indicate defective fatty acid metabolism in these two patients. It is, however, not known whether the abnormal mitochondrial ultrastructure represents a primary abnormality or secondary to defective fatty acid metabolism.