Activation of cortical areas is accompanied by a depolarization of neurone membrane potentials. Neuronal activation leads to more increase in local blood flow than expected from oxygen consumption, and thus to an increase of oxygenated hemoglobin in the capillaries of activated brain tissue. These changes of the local blood supply and the magnetic properties of blood can be visualized via magnetic resonance imaging (MRI). One should keep in mind that electronically applied stimulation signals may be distorted by the MR tomograph (MRT). The key signals should be recorded and saved by a PC via an electro-optic transducer. The size of the cortical area which represents movements is not proportional to the size and strength of the muscle group involved but to the degree of differentiation and specialization for the type of movement. The concept of a somatotopic organization of the primary motor cortex (M1) is probably only adequate in a gross approximation. Tongue movements produced symmetrical activation at the lower primary motor cortex. During automatic speech a strong functional lateralization to the left hemisphere emerged within the same area. The severity of structural damage to hand motor projections of the cortico-spinal tract was assessed on semi-coronal MRI reconstructions along anatomical landmarks of cortico-spinal tract. The functional integrity of these crossed cortico-spinal projections in the affected hemisphere, as well as the presence of any abnormal ipsilateral projections to the paretic hand, was examined by transcranial magnetic stimulation (TMS). Cortical activation during simple voluntary hand movements was studied by functional magnetic resonance imaging (fMRI). The presented fMRI results on functional anatomy of the motor system and of cortical networks engaged in language production as well as the detected cortical reorganization after acquired brain lesions should convince the reader that the fMRI method can reliably be used to address neuroscientific questions and safely be applied in a clinical setting.