We measured the peak voltage induced in a sensing loop by a Magstim 200 magnetic stimulator. Coil output varied little for repeated stimulation at the same intensity over a wide range of coil output. In contrast, the first stimulus immediately after a change in intensity was of larger amplitude and showed greater variability than subsequent stimuli. The effect was seen for changes in intensity of 5% and 60% and was greater for reductions than for increases in stimulation intensity. Stimulation immediately after a reduction in intensity from 100% to 40% resulted in peak induced voltages as high as those recorded for repeated stimulation at 43% of maximum coil output. Increased coil output following changes in stimulation intensity may affect measurement of the threshold old for motor cortical stimulation. The effect of a change in intensity could be minimized by delaying stimulation for at least 30 s or discarding the first stimulus after the change.