Blood oxygenation level dependent functional magnetic resonance imaging (BOLD fMRI), because of its superior resolution and unlimited repeatability, can be particularly useful in studying functional aspects of the human motor system, especially plasticity, and somatotopic and temporal organization. In this survey, while describing studies that have reliably used BOLD fMRI to examine these aspects of the motor system, we also discuss studies that investigate the neural substrates underlying motor skill acquisition, motor imagery, production of motor sequences; effect of rate and force of movement on brain activation and hemispheric control of motor function. In the clinical realm, in addition to the presurgical evaluation of neurosurgical patients, BOLD fMRI has been used to explore the mechanisms underlying motor abnormalities in patients with neuropsychiatric disorders and the mechanisms underlying reorganization or plasticity of the motor system following a cerebral insult.