The present chapter reports the current knowledge on the use of functional MRI (fMRI) in patients with atypical parkinsonisms, including Multiple System Atrophy, Corticobasal Syndrome and Progressive Supranuclear Palsy syndrome. Both resting state functional connectivity and task-based brain activity abnormalities are reported in atypical parkinsonisms relative to healthy controls and Parkinson's disease patients. Functional alterations were observed earlier than structural damage and may help to make early diagnosis. The chapter also examines the few longitudinal evidence on fMRI changes in patients with these conditions. The potential use of fMRI techniques in aiding the differential diagnosis, accurately measuring disease progression and assessing the effectiveness of therapeutic interventions is discussed. © 2018 Elsevier Inc.