Multiple system atrophy is a neurodegenerative disease, which is characterized by a combination of autonomic failure, Parkinsonian features, pyramidal and cerebellar dysfunction, and is poorly reactive to levodopa. Few biomarkers with high sensitivity or specificity have been applicable in the diagnosis of multiple system atrophy, making it a challenge to correctly diagnose this disease. Therefore, some researches combined several biomarkers to improve the diagnosis accuracy. Apart from those in body fluid, progress has been made in new biomarkers of neuroimaging and pathology. In this review, the advances in the identification of biomarkers of multiple system atrophy are summarized, and some candidate biomarkers that worth more investigation, including proteins and miRNAs in blood or cerebrospinal fluid, parameters in molecular and functional imaging, and pathologic features of peripheral tissue are described .