Magnetic stimulation of the human brain is performed in clinical and research settings, but the site of activation has not been clearly localized in humans or other species. We used a set of magnetic stimulus coils with different field profiles to isolate movement of single digits at motor threshold and to calculate corresponding electric field strengths at various distances beneath the scalp. Two coils could produce the same electric field intensity at only 1 point. Thus, we could estimate the depth of stimulation by finding the intersection of the electric field plots, which were then superimposed on MRIs of the underlying brain. In each of 3 subjects the field plots intersected at the crown of a gyrus, in the region of the central sulcus, an near the level of the gray-white junction. This position and the electric field orientation support localization to layer VI of cerebral cortex.