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Multiple system atrophy (MSA) and Parkinson's disease (PD) exhibit distinct patterns of autonomic dysfunction, but differences in sudomotor function remain incompletely characterized. We investigated whether electrochemical skin conductance (ESC) measured by Sudoscan provides autonomic information complementary to ¹²³I-metaiodobenzylguanidine (MIBG) myocardial scintigraphy. We retrospectively analyzed 15 patients with MSA (12 MSA-C, 3 MSA-P) and 48 with PD who underwent Sudoscan after excluding patients with diabetes mellitus or Sjögren's syndrome; MIBG data were available in 9 and 43 patients, respectively. The feet-hands ESC gradient was designated as the primary outcome for the present analyses. The gradient was significantly lower in MSA than in PD (median -3.5 vs. 10.9 μS, p < 0.001), and feet ESC was lower in MSA (63.7 vs. 77.7 μS, p = 0.005), whereas hands ESC did not differ significantly. A negative gradient was observed in 53% of patients with MSA and 8% with PD. MIBG myocardial scintigraphy showed relatively preserved cardiac sympathetic innervation in MSA compared with PD (delayed H/M ratio 3.67 vs. 1.49, p < 0.001). Exploratory analyses showed no significant correlations between the ESC gradient and disease duration, available clinical severity measures, or MIBG parameters. These findings suggest that Sudoscan and MIBG myocardial scintigraphy provide complementary information for autonomic phenotyping in parkinsonian disorders.