Abstract In order to identify the neurochemical alterations in motor associated subcortical nuclei, and enhance our understanding of neurophysiology of progressive reduction in fine motor control with aging, the metabolic changes in striatum and cerebellar cortex in SD rats along with aging were investigated using a metabonomic approach based on high resolution “magic angle spinning” 1H-NMR spectroscopy and partial least squares-discriminant analysis. It was found that there were increased myo-inositol and lactate, and decreased taurine in these two brain regions of old rats. The above changes may be a marker for alterations of neuronal cells, which reduce fine motor control. Besides, some of the metabolites are gender-related and region-specific. Old female rats had decreased glutamate and increased creatine in striatum, while old male rats had increased choline in striatum, and increased GABA in cerebellar cortex, respectively. However, further analyses showed that most of the metabolites in male rats were not distinctively different with those of female ones except choline, which was in a relative lower level in striatum of male rats. All this results suggest that energy metabolism is an important indication of age-related change, which is not only in male, but also in female rats.