A system and method is disclosed that can be used to track and navigate an instrument relative to a patient. The system can include an electromagnetic tracking system to track an electromagnetic stimulation probe, such as a transcranial magnetic stimulation probe. The system can, according to various embodiments, provide a tracking device on the probe, track the coil of the probe, provide a field relative to the probe, and determine the position of the patient based upon the field produced by the probe.
