Neuroimaging has become more important for multiple system atrophy (MSA) clinically as well as in research studies. This chapter focuses on structural MR techniques such as conventional magnetic resonance imaging (cMRI) including standard T1- and T2-weighted as well as fluid-attenuated inversion recovery (FLAIR) sequences. It also focuses on different advanced MR techniques including methods to assess regional cerebral atrophy quantitatively, such as magnetic resonance volumetry (MRV), diffusion-weighted imaging and diffusion tensor imaging (DWI/DTI), as well as magnetization transfer imaging (MTI). As an indirect method of measuring regional brain atrophy, groups have applied simple quantitative measures of diameters, areas, and volumes including region of interest (ROI)-based assessment of various structures on MRI for differential diagnostic purposes. A summary of these methods and their diagnostic accuracy for MSA is provided in the chapter; the methods include: MR-planimetry, -volumetry, and voxel-based morphometry (VBM).