BACKGROUND: Multiple system atrophy (MSA) and idiopathic Parkinson's disease (IPD) are two common neurodegenerative disorders presenting with parkinsonism. Since a brain MRI study is an available method for differentiating MSA from IPD, we tried to find further values of brain MRI studies in differentiating MSA from IPD. METHODS: We measured anteroposterior and transverse diameters (AD and TD, respectively) of the brain stem of T2-weighted axial images. We graded the severity of atrophy (grade 0: none; grade 1: mild; grade 2: moderate; and grade 3: severe) of cerebellar vermis and hemispheres on the midsagittal and parasagittal planes. RESULTS: There were 36 patients with probable MSA and 40 patients with IPD. We calculated a parameter multiplying AD of the midbrain by TD of the midbrain. The mean of the AD x TD of the midbrain was 1007.5 +/- 161.8 mm2 in patients with MSA, and it was significantly smaller than that of those with IPD (1113.3 +/- 118.7 mm2). When the cut off value was decided as 1050 mm2, the sensitivity of the parameter for the diagnosis of MSA was 83.3% and specificity was 80%. The frequency of cerebellar atrophy was 72.2% in patients with MSA, and it was significantly higher than that of those with IPD (37.5%). CONCLUSIONS: Measurements of the brain stem, particularly the midbrain, and cerebellum areas on brain MRI are helpful methods for the differential diagnosis of patients with MSA from those with IPD.