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Abstract Harmony is one of the most fundamental elements of music that evokes emotional response. The inferior colliculus (IC) has been known to detect poor agreement of harmonics of sound, that is, dissonance. Electrophysiological evidence has implicated a relationship between a sustained auditory response mainly from the brainstem and unpleasant emotion induced by dissonant harmony. Interestingly, an individual’s dislike of dissonant harmony of an individual correlated with a reduced sustained auditory response. In the current paper, we report novel evidence based on functional magnetic resonance imaging (fMRI) for such a relationship between individual variability in dislike of dissonance and the IC activation. Furthermore, for the first time, we show how dissonant harmony modulates functional connectivity of the IC and its association with behaviourally reported unpleasantness. The current findings support important contributions of low level auditory processing and corticofugal interaction in musical harmony preference.