To determine the stimulation site of both facial and hypoglossal nerves after transcranial magnetic stimulation.After surgical exposure of the brainstem in 22 patients with intrinsic pontine (n=9) or medullary (n=13) tumors, the facial colliculus and the hypoglossal triangle were electrically stimulated. The EMG responses were recorded with flexible wire electrodes from the orbicularis oculi/orbicularis oris muscles, and genioglossal muscles. Patients had no preoperative deficit of the nerves.The EMG mean latencies of the unaffected facial nerve were 5.2+/-0.6 ms for the orbicularis oculi, and 5.2+/-0.5 ms for the orbicularis oris muscle. After the stimulation of 18 possibly affected facial nerves, the EMG mean latencies were 5.3+/-0.3 ms for the orbicularis oculi (p=0.539, unpaired Student's t-test), and 5.4+/-0.2 ms for the orbicularis oris (p=0.122). The EMG mean latency of the unaffected hypoglossal nerve was 4.1+/-0.6 ms for the genioglossal muscle. After the stimulation of 26 possibly affected hypoglossal nerves, the EMG mean latency for the genioglossal muscle was 5.3+/-0.3 ms. There was a significant difference (p<0.001) in latency for genioglossal EMG responses between the patients with pontine and those with medullary tumors.Shorter EMG mean latencies of unaffected facial nerves obtained after direct stimulation of the facial colliculi confirm that magnetic stimulation is most likely to occur closer to the nerve's exit from the brainstem than to its entrance into the internal auditory meatus. The hypoglossal nerve seems to have the site of excitation at the axon hillock of the hypoglossal motor neurons.