The aim of this study was to evaluate motor cortex excitability in spinocerebellar ataxia type 2 (SCA2). Cortical silent period (CSP), motor thresholds, and intracortical inhibition and facilitation by paired transcranial magnetic stimulation (TMS) were investigated in 18 SCA2 patients and in 20 controls. The mean CSP duration and motor threshold after TMS were significantly increased in the patient group. Intracortical inhibition by paired TMS at short interstimulus intervals (ISIs) showed no significant differences between patients and controls; at longer ISIs, the expected facilitation of test responses, observed in control subjects, resulted significantly less marked in SCA2 patients at all the tested intervals. Our findings extend previous findings on cerebellar dysfunctions of varying aetiologies by investigating intracortical excitability in SCA2. In addition, this study demonstrates that the cortical excitability involvement found in SCA2 is independent on the cytosine-adenine-guanine repeat expansion. The neurophysiological alterations seen in our patients relate to the worsening of general clinical condition. Thus, we might speculate that changes of motor cortex excitability in SCA2 represent a slow neurodegenerative process characterized by gradual loss of cerebellar neurons leading to an increasing disturbance of the balance between inhibitory and excitatory circuits in the motor system.