During the last decades, transcranial magnetic stimulation (TMS) has been used as a noninvasive method to investigate motor cortical reorganization and neuroplasticity in humans after stroke. An increasing number of studies in the field of motor control have used TMS to gain an understanding of the different aspects of stroke cortical physiology and motor recovery. This review addresses the effects of corticospinal tract (CST) lesions in humans and nonhuman primates on the functional organization of the motor system. We review information on the physiological mechanisms by which the CST contributes to normal motor control and to central nervous system reorganization following stroke when the CST is injured as measured using TMS. Insight into these physiological mechanisms has led to the development of scientifically sound interventional proposals in the field of neurorehabilitation.