Some combinations of musical notes sound pleasing and are termed “consonant,” but others sound unpleasant and are termed “dissonant.” The distinction between consonance and dissonance plays a central role in Western music, and its origins have posed one of the oldest and most debated problems in perception. In modern times, dissonance has been widely believed to be the product of “beating”: interference between frequency components in the cochlea that has been believed to be more pronounced in dissonant than consonant sounds. However, harmonic frequency relations, a higher-order sound attribute closely related to pitch perception, has also been proposed to account for consonance. To tease apart theories of musical consonance, we tested sound preferences in individuals with congenital amusia, a neurogenetic disorder characterized by abnormal pitch perception. We assessed amusics’ preferences for musical chords as well as for the isolated acoustic properties of beating and harmonicity. In contrast to control subjects, amusic listeners showed no preference for consonance, rating the pleasantness of consonant chords no higher than that of dissonant chords. Amusics also failed to exhibit the normally observed preference for harmonic over inharmonic tones, nor could they discriminate such tones from each other. Despite these abnormalities, amusics exhibited normal preferences and discrimination for stimuli with and without beating. This dissociation indicates that, contrary to classic theories, beating is unlikely to underlie consonance. Our results instead suggest the need to integrate harmonicity as a foundation of music preferences, and illustrate how amusia may be used to investigate normal auditory function.