Recent studies have reported that the majority of patients with multiple system atrophy (MSA) had hypertensive heart disease. However, the effect of autonomic failure on the brain in MSA has not been studied. We consecutively enrolled 63 patients with MSA and selected 63 age- and sex-matched healthy subjects. We performed a comparative analysis of cerebrovascular lesions between the patients with MSA and the control subjects and analyzed predisposing factors for cerebrovascular lesions in the patients with MSA. There was no significant difference in lacune and territorial infarcts between the patients with MSA and the control subjects. The median grading score of white matter hyperintensity (WMH) was significantly higher in the patients with MSA (1.0, interquartile range 0.5-2.0) than the control subjects (0.0, interquartile range 0.0-1.0; P < 0.01). In the patients with MSA, there was strong correlation between the grading score of WMH and supine systolic blood pressure (r = 0.529, P < 0.001) after adjusting for age. Multiple linear regression analysis showed that age and supine systolic blood pressure was significantly and independently correlated with the grading score of WMH. The present study demonstrates that patients with MSA had more severe WMH and that supine systolic pressure is a major contributing factor for the severity of WMH, suggesting that patients with MSA have target-organ damage of the brain.