At disease onset clinically, the motor symptoms and signs are usually asymmetric or unilateral in majority of Parkinson’s disease (PD) patients. When disease progresses to a later stage, the asymmetry becomes less significant. The cause of this asymmetry, and the relationship between functional deficits and the structural changes in the brain are not clear. In this study, we investigated the morphological changes in the brain hemispheres corresponding to the early-onset and late-onset body sides through a longitudinal study on 24 early-stage PD patients. Significant atrophy was observed in the motor cortex and basal ganglia nuclei.