Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder mapped on chromosome 12. Different results have been reported in spinocerebellar ataxias following transcranial magnetic stimulation (TMS). TMS-induced cortical silent period (CSP) was prolonged in different cerebellar disorders. Here we evaluate the duration of the TMS-induced CSP following a single magnetic stimulus in a large homogeneous group of SCA2 patients compared with idiopathic cerebellar ataxia (IDCA) patients with similar disease duration and severity, and in 20 healthy controls. The CSP duration in both arm and leg muscles was significantly (p<0.005) longer in patients than in controls. A significant positive correlation between disease duration and CSP prolongation in both SCA2 and IDCA was found. No correlation between age, onset and CSP duration emerged in either group. This study shows a prolongation of the TMS-induced silent period in both SCA2 and IDCA indicating that the cortical inhibitory mechanism is dependent on the disease duration and severity. Thus, the cerebellum seems to exert a pliable physiological influence on the cortico-spinal system through control of inhibitory cortical interneurons.