Parkinson's disease (PD) is associated with changes in the substantia nigra, which communicates with subcortical nuclei. This study investigates subcortical nuclei volume in PD in vivo by magnetic resonance (MR) imaging. Caudate, putaminal, and thalamic nuclei were measured on axial MR images using a point counting method and systematic sampling. PD patients (n = 21) had significantly smaller subcortical nuclei than age- and sex-matched controls (p < 0.001) and depressed patients (p < 0.01). The decline in PD was not correlated with age, sex, or cortical volume. Depressed patients had significantly smaller caudate and putaminal nuclei than controls (p < 0.05 and 0.01, respectively) but thalamic nuclei were not significantly different. Caudate, putaminal, and thalamic nuclei volumes of controls were significantly negatively correlated with age (r = -0.58, p < 0.01; r = -0.77, p < 0.001; r = -0.57, p < 0.01, respectively). Depressed subjects demonstrated a negative trend. Volumetric measurements by MR imaging may be a useful in investigating the role of the basal ganglia in neurological disorders.