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Differentiation of multiple system atrophy with predominant parkinsonism (MSA-P) and Parkinson's disease (PD) is important, but an effective tool for differentiation has not been identified. We investigated the efficacy of the composite autonomic symptom scale 31 (COMPASS 31) questionnaire as a tool for evaluating autonomic function in parkinsonism patients. In this study, we enrolled drug-naïve patients with MSA-P and PD, and administered the COMPASS-31 and an objective autonomic dysfunction test (AFT). Demographic and clinical data, including parkinsonism and autonomic dysfunction, were compared between the two groups. Additionally, we determined the optimal COMPASS 31 cut-off score to differentiate MSA-P from PD for use as a screening tool. In this study, 27 MSA-P patients and 41 PD patients were recruited. The total COMPASS 31 score was well correlated with the objective AFT results. When we compared the COMPASS 31 score between the two groups, MSA-P patients showed higher total scores and sub-scores in the orthostatic intolerance, gastrointestinal, and bladder domains compared with PD patients. Similarly, MSA-P patients had more abnormalities in expiration to inspiration ratio, Valsalva ratio and pressure recovery time than PD patients in objective AFT. With 13.25 as the cut-off score for diagnosis of MSA-P, the total COMPASS-31 score demonstrated high sensitivity (92.6%) and moderate specificity (51.2%) with an area under the curve of 0.765. Based on our results, the COMPASS 31 is an effective tool for evaluation of autonomic function in patients with parkinsonism. The COMPASS-31 could be used as a sensitive and convenient screening tool, especially for the differentiation between MSA-P and PD.