In this study, we evaluated the characteristics of the brain in a genetically modified marmoset model of Parkinson’s disease. Various contrast images were acquired using magnetic resonance imaging (MRI), and the whole brain underwent explorative investigation with each contrast. For each image, statistical evaluation was performed using SPM. Diffusion tensor MRI showed significance differences in the thalamus, while magnetization transfer ratio images showed a significant difference in the nigral striatum. The findings suggest that the marmoset is useful as a model animal to study human diseases.