Motor threshold is a means of quantifying stimulus in transcranial magnetic stimulation. Two methods are used. One involves neurophysiology techniques and the other is visualization of movement. The aim was to compare the percentage of total machine output (PTMO) necessary to achieve motor threshold using these different methods. Neurophysiological and visualization of movement thresholds were determined in six subjects. In all subjects, the two thresholds were achieved with a <10% difference in PTMO. Determination of motor threshold with a neurophysiological and a visualization of movement method produced similar results.