The motor system has been intensively studied using the emerging neuroimaging technologies over the last twenty years. These include early applications of positron emission tomography of brain perfusion, metabolic rate and receptor function, as well as functional magnetic resonance imaging, tractography from diffusion weighted imaging, and transcranial magnetic stimulation. Motor system research has the advantage of the existence of extensive electrophysiological and anatomical information from comparative studies which enables cross-validation of new methods. We review the impact of neuroimaging on the understanding of diverse motor functions, including motor learning, decision making, inhibition and the mirror neuron system. In addition, we show how imaging of the motor system has supported a powerful platform for bidirectional translational neuroscience. In one direction, it has provided the opportunity to study safely the processes of neuroplasticity, neural networks and neuropharmacology in stroke and movement disorders and offers a sensitive tool to assess novel therapeutics. In the reverse direction, imaging of clinical populations has promoted innovations in cognitive theory, experimental design and analysis. We highlight recent developments in the analysis of structural and functional connectivity in the motor system; the advantages of integration of multiple methodologies; and new approaches to experimental design using formal models of cognitive-motor processes.