In recent years, our understanding of motor learning, neuroplasticity and functional recovery after the occurrence of brain lesion has grown significantly. Novel findings in basic neuroscience have provided an impetus for research in motor rehabilitation. The brain reveals a spectrum of intrinsic capacities to react as a highly dynamic system which can change the properties of its neural circuits. This brain plasticity can lead to an extreme degree of spontaneous recovery and rehabilitative training may modify and boost the neuronal plasticity processes. Animal studies have extended these findings, providing insight into a broad range of underlying molecular and physiological events. Neuroimaging studies in human patients have provided observations at the systems level that often parallel findings in animals. In general, the best recoveries are associated with the greatest return toward the normal state of brain functional organization. Reorganization of surviving central nervous system elements supports behavioral recovery, for example, through changes in interhemispheric lateralization, activity of association cortices linked to injured zones, and organization of cortical representational maps. Evidence from animal models suggests that both motor learning and cortical stimulation alter intracortical inhibitory circuits and can facilitate long-term potentiation and cortical remodeling. Current researches on the physiology and use of cortical stimulation animal models and in humans with stroke related hemiplegia are reviewed in this article. In particular, electromyography (EMG)-controlled electrical muscle stimulation improves the motor function of the hemiparetic arm and hand. A multi-channel near-infrared spectroscopy (NIRS) studies in which the hemoglobin levels in the brain were non-invasively and dynamically measured during functional activity found that the cerebral blood flow in the injured sensory-motor cortex area is greatest during an EMG-controlled FES session. Only a few idea is, however, known for the optimal timing of the different processes and therapeutic interventions and for their interactions in detail. Finding optimal rehabilitation paradigms requires an optimal organization of the internal processes of neural plasticity and the therapeutic interventions in accordance with defined plastic time windows. In this review the mechanisms of spontaneous plasticity after stroke and experimental interventions to enhance plasticity are summarized, with an emphasis on functional electrical stimulation therapy.