Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive electrophysiological method to modulate cortical excitability. As such, rTMS can be used in conjunction with conventional physiotherapy or occupational therapy to facilitate rehabilitation of motor function in patients with focal brain lesions. This review summarizes the rationale for using rTMS in the rehabilitation of motor deficits as derived from imaging and electrophysiological studies of the human motor system. rTMS methodology and its various stimulation modalities are introduced and current evidence for rTMS as supportive therapy for the rehabilitation of chronic motor deficits is discussed.