An electrophysiological measurement method and system is provided for positioning an implantable transducer of a hearing instrument relative to a middle ear component or inner ear of a patient. The method and system employ electrophysiological measurement signals obtained in response to test signals applied to an implanted transducer. In one embodiment, the electrophysiological measurements are obtained by an electrocochleography measurement device that measures the cochlear summating potential and/or action potential responsive to test signals applied to an implanted transducer. In another embodiment, an auditory brainstem response measurement device is utilized to obtain electrical potential measurement signals responsive to test signals applied to an implanted transducer.