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Background and Purpose: Multiple system atrophy(MSA) is a rare adult‐onset synucleinopathy that can be divided in two subtypes depending on whether the prevalence of its symptoms is more parkinsonian or cerebellar (MSA‐P and MSA‐C, respectively). The aim of this work is to investigate the structural MRI changes able to discriminate MSA phenotypes. Methods: The sample includes 31 MSA patients (15 MSA‐C and 16 MSA‐P) and 39 healthy controls. Participants underwent a comprehensive motor and neuropsychological battery. MRI data were acquired with a 3T scanner (MAGNETOM Trio, Siemens, Germany). FreeSurfer was used to obtain volumetric and cortical thickness measures. A Support Vector Machine (SVM) algorithm was used to assess the classification between patients' group using cortical and subcortical structural data. Results: After correction for multiple comparisons, MSA‐C patients had greater atrophy than MSA‐P in the left cerebellum, whereas MSA‐P showed reduced volume bilaterally in the pallidum and putamen. Using deep gray matter volume ratios and mean cortical thickness as features, the SVM algorithm provided a consistent classification between MSA‐C and MSA‐P patients (balanced accuracy 74.2%, specificity 75.0%, and sensitivity 73.3%). The cerebellum, putamen, thalamus, ventral diencephalon, pallidum, and caudate were the most contributing features to the classification decision (z > 3.28; p <.05 [false discovery rate]). Conclusions: MSA‐C and MSA‐P with similar disease severity and duration have a differential distribution of gray matter atrophy. Although cerebellar atrophy is a clear differentiator between groups, thalamic and basal ganglia structures are also relevant contributors to distinguishing MSA subtypes. [ABSTRACT FROM AUTHOR]