Theory of Mind is defined as the ability to attribute mental state and emotions to other people and is relevant to social relationships. The cortical and subcortical regions involved in Theory of Mind are damaged by neurodegenerative processes of Parkinsonian syndromes, so the aim of the present study was to explore, for the first time, possible deficits of Theory of Mind and their cognitive correlates in multiple system atrophy (MSA). Twenty-six patients with MSA, 25 patients with Parkinson’s disease (PD) and 25 healthy subjects were enrolled. Cognitive and affective subcomponents of Theory of Mind, executive functions, long-term memory and apathy were evaluated. The three groups did not differ on demographic variables. MSA and PD groups performed worse than healthy subjects on both cognitive (advanced test of ToM) and affective (emotion attribution task) ToM tasks, but no significant difference was found between patients’ groups. However, when using another affective ToM task (Eyes Test), MSA group had poorer performance than healthy subjects and Parkinsonian patients, whereas Parkinsonian patients had similar performance to healthy subjects. Regression analysis revealed an association between poor cognitive flexibility and dysfunctional cognitive component of Theory of Mind. Deficit of cognitive and affective components of Theory of Mind occurred in MSA. Dysfunction of cognitive component was related to executive dysfunction (i.e. cognitive rigidity). These findings might suggest the usefulness of an early evaluation of social cognition in MSA to identify individuals with impaired Theory of Mind who are at risk of social withdrawal, and reduced quality of life.