Historically, studies have extensively examined the basal ganglia in Parkinson’s disease for specific characteristics that can be observed with medical imaging. One particular methodology used for detecting changes that occur in Parkinson’s disease brains is diffusion tensor imaging, which yields diffusion indices such as fractional anisotropy and radial diffusivity that have been shown to correlate with axonal damage. In this study, we compare the diffusion measures of basal ganglia structures (with substantia nigra divided into subregions, pars compacta, and pars reticula), as well as the diffusion measures of the diffusion tracts that pass through each pair of basal ganglia structures to see if significant differences in diffusion measures can be observed in structures or tracts in newly diagnosed Parkinson’s disease patients. Additionally, we include the ventral tegmental area, a structure connected to various basal ganglia structures affected by dopaminergic neuronal loss and have historically shown significant alterations in Parkinson’s disease, in our analysis. We found significant fractional anisotropy differences in the putamen, and in the diffusion tracts that pass through pairs of both substantia nigra subregions, subthalamic nucleus, parabrachial pigmental nucleus, ventral tegmental area. Additionally, we found significant radial diffusivity differences in diffusion tracts that pass through the parabrachial nucleus, putamen, both substantia nigra subregions, and globus pallidus externa. We were able to find significant diffusion measure differences in structures and diffusion tracts, potentially due to compensatory mechanisms in response to dopaminergic neuronal loss that occurs in newly diagnosed Parkinson’s disease patients.