We used focal transcranial magnetic stimulation to examine the effects of 120 synchronized thumb and foot movements on the motor output map of the right abductor pollicis brevis muscle (APB) (experiment 1). To evaluate the performance, the latencies between the onset of the electromyographic activity (EMG) of the two muscles were measured. As control, 120 asynchronous thumb and foot movements were performed (experiment 2). Exclusively in experiment 1, the center of gravity (CoG) of the output map moved medially in the direction of the foot representation area (mean 7 mm, P<0.05) and returned into its original location within 1 h. In experiment 2, the CoG remained unchanged (mean displacement, 0.68 mm into a lateral direction; not significant). The effect in experiment 1 was independent of an improvement in performance. We conclude that a short-lasting training of synchronous movements induces modulations of motor output maps which probably occur due to interactions between hand and foot representation areas in the motor cortex.