The cortical processing of musical sounds is influenced by listeners’ sensitivity to the structural regularities of music, and particularly by sensitivity to harmonic relationships. As subcortical and cortical processing dynamically interact to shape auditory perception in an experience-dependent manner, we asked whether subcortical processing of musical sounds would be sensitive to harmonic relationships. We examined auditory brainstem responses to a chord that was preceded either by a harmonically related chord, by an unrelated chord, or was repeated. We observed higher spectral response magnitudes in the related than in the unrelated or repeated conditions, for both musician and nonmusician listeners. Our results suggest that listeners’ implicit knowledge of musical regularities influences subcortical auditory processing.