Neurofilament light chain (NFL) in blood has been identified as a valuable biomarker in multiple system atrophy (MSA), but data regarding its utility in the early diagnosis and prognosis of MSA remain limited.To investigate serum NFL's diagnostic and prognostic value in patients with MSA in a prospective clinical cohort.Two hundred twenty-eight participants were enrolled, including ninety-eight with MSA, seventeen with uncertain MSA at inclusion, fifty-nine with Parkinson's disease (PD), and fifty-four healthy controls (HCs). Patients with MSA and uncertain diagnoses were followed up. Serum NFL levels were measured with electrochemiluminescence immunoassay at baseline.Patients with MSA and uncertain diagnoses underwent repeated clinical assessments with a median follow-up period of 1.43 years. The final diagnoses included 102 MSA, 62 PD, and 54 HCs. Serum NFL levels were significantly higher in MSA and PD than in HCs. Serum NFL levels, with cutoff values of 223.5 and 218.0 pg/mL, could discriminate between patients with MSA and PD (AUC = 0.930) in the early disease stages, and between MSA-parkinsonism subtypes and PD (AUC = 0.878). Higher serum NFL levels were independently associated with a shorter median time to poor prognosis and death. In addition, reduced levodopa responsiveness was correlated with poor outcomes, and orthostatic hypotension (OH) was linked to a higher risk of death.Serum NFL levels can not only differentiate between MSA, MSA-P, and PD in the early stages of the disease but also serve as a reliable independent predictor of poor prognosis and survival time in MSA.© 2024. Springer-Verlag GmbH Germany, part of Springer Nature.