In this review, we describe how different neuroimaging tools have been used to identify novel MSA biomarkers, highlighting their advantages and limitations. First, we describe the main structural MRI changes frequently associated with MSA including the ‘hot cross-bun’ and ‘putaminal rim’ signs as well as putaminal, pontine, and middle cerebellar peduncle (MCP) atrophy. We discuss the sensitivity and specificity of different supra- and infratentorial changes in differentiating MSA from other disorders, highlighting those that can improve diagnostic accuracy, including the MCP width and MCP/superior cerebellar peduncle (SCP) ratio on T1-weighted imaging, raised putaminal diffusivity on diffusion-weighted imaging, and increased T2* signal in the putamen, striatum, and substantia nigra on susceptibility-weighted imaging. Second, we focus on recent advances in structural and functional MRI techniques including diffusion tensor imaging (DTI), resting-state functional MRI (fMRI), and arterial spin labelling (ASL) imaging. Finally, we discuss new approaches for MSA research such as multimodal neuroimaging strategies and how such markers may be applied in clinical trials to provide crucial data for accurately selecting patients and to act as secondary outcome measures.