Multiple system atrophy (MSA) including striatonigral degeneration (SND) and olivopontocerebellar atrophy (OPCA) is a group of heterogeneous degenerative neurological disorders, which differ from the idiopathic Parkinson’s disease (IPD) in certain clinical features. The differential diagnosis between IPD and MSA is difficult because of the common of signs and symptoms common. The purpose of this study was comparison of cerebral glucose metabolic differences of SND, OPCA and IPD. The 18F-FDG PET images of SND, OPCA and IPD patients were assessed by statistical pattern analysis using statistical parametric mapping (SPM) and image registration in order to determine the useful metabolic patterns. A total of 11 patients with MSA (5 SND: mean age 61.6±8.3 y, M/F 1/4; 6 OPCA: mean age 55.3±8.4 y, M/F 3/3), 8 patients (mean age 67.9 10.7y; M/F: 3/5) with IPD were enrolled in this study. All subjects and 22 age matched normal controls underwent 18F-FDG PET. Each of the SND, OPCA and IPD patients were individually compared with the normal control group using a two-sided t-test for SPM (P<0.05). The OPCA group showed significant hypometabolism in the cerebellum and pons compared to the control group, whereas in the patients with SND showed significant hypometabolism in the putamen. SPM also revealed pons, putamen hypometabolism in OPCA and SND patients compared with IPD patients. An assessment of the 18F-FDG PET images using the image registration and statistical analysis might be a useful adjunct to a clinical examination when making a differential diagnosis of Parkinsonism.