In patients with cerebellar ataxia, several abnormalities in cortical excitability by TMS had been observed. The aim of this study is to investigate the neurophysiological effect on the motor cortex after high frequency rTMS on motor cortex in patients with spinocerebellar degeneration (SCD). I waves facilitation and Intracortical inhibition in patients with cerebellar ataxia by a paired-pulse TMS was studied. And Cortical effect after 5Hz-rTMS on motor cortex was evaluated. I waves facilitation was significantly reduced in SCD, whereas for intracortical inhibition no significant change was found. 5Hz-rTMS on motor cortex can have some cortical facilitatory effect in SCD patients. Our study suggests high-frequency rTMS could have the neuromodulatory tool in patients with SCD.