Musicians have a variety of perceptual and cortical specializations compared to non-musicians. Recent studies have shown that potentials evoked from primarily brainstem structures are enhanced in musicians, compared to non-musicians. Specifically, musicians have more robust representations of pitch periodicity and faster neural timing to sound onset when listening to sounds or both listening to and viewing a speaker. However, it is not known whether musician-related enhancements at the subcortical level are correlated with specializations in the cortex. Does musical training shape the auditory system in a coordinated manner or in disparate ways at cortical and subcortical levels? To answer this question, we recorded simultaneous brainstem and cortical evoked responses in musician and non-musician subjects. Brainstem response periodicity was related to early cortical response timing across all subjects, and this relationship was stronger in musicians. Peaks of the brainstem response evoked by sound onset and timbre cues were also related to cortical timing. Neurophysiological measures at both levels correlated with musical skill scores across all subjects. In addition, brainstem and cortical measures correlated with the age musicians began their training and the years of musical practice. Taken together, these data imply that neural representations of pitch, timing and timbre cues and cortical response timing are shaped in a coordinated manner, and indicate corticofugal modulation of subcortical afferent circuitry.