Transcranial magnetic stimulation has gained increasing visibility as an evaluative and interventional tool during the past 15 years. Within the context of rehabilitation, transcranial magnetic stimulation has been applied to differentiate excitatory and inhibitory mechanisms and to assess cortical reorganization following specific interventions. This article reviews some of the more salient features of transcranial magnetic stimulation applications relevant to stroke rehabilitation, highlighting the strengths and weaknesses in this approach. Data derived from such studies may be profoundly over-interpreted. Information is provided showing the importance of utilizing fundamental principles of electrode placement and kinesiological electromyography to more accurately reflect and interpret data emerging from transcranial magnetic stimulation mapping studies, particularly as they apply to the interpretation of cortical reorganization following application of neurorehabilitative procedures.