Because the progression of multiple system atrophy (MSA) is usually rapid and there still is no effective cause-related therapy, early and accurate diagnosis is important for the proper management of patients as well as the development of neuroprotective agents. However, despite the progression in the field of MSA research in the past few years, the diagnosis of MSA in clinical practice still relies largely on clinical features and there are limitations in terms of sensitivity and specificity, especially in the early course of the disease. Furthermore, recent pathological, clinical, and neuroimaging studies have shown that (1) MSA can present with a wider range of clinical and pathological features than previously thought, including features considered atypical for MSA; thus, MSA can be misdiagnosed as other diseases, and conversely, disorders with other etiologies and pathologies can be clinically misdiagnosed as MSA; and (2) several investigations may help to improve the diagnosis of MSA in clinical practice. These aspects should be taken into consideration when revising the current diagnostic criteria. This is especially true given that disease-modifying treatments for MSA are under investigation.