We investigated clinical and MRI correlation in 18 patients with clinically-diagnosed multiple system atrophy (MSA) and 16 age-matched controls, using 1.5 T magnetic resonance imaging (MRI). We evaluated the severity of parkinsonism in each MSA patient. In assessing the MRI findings, we examined three parameters quantitatively: width of the pars compacta of the substantia nigra (SNc); putaminal hypointensity on T2-weighted images; and putaminal atrophy. As in previous studies, SNc width was narrowed and the putaminal signal intensity was decreased in patients with MSA compared with controls. The clinical severity of parkinsonism did not correlate significantly with the SNc width or the score of putaminal hypointensity in MSA. However, not only did putaminal atrophy occur, but correlated well with the severity of parkinsonism in MSA. A significant correlation could not be established between narrowing of SNc and shrinkage of the putamen. These findings suggest that putaminal atrophy is associated with the clinical manifestations of parkinsonism and do not support the hypothesis that transsynaptic degeneration occurs in MSA.