Most natural sounds are composed of a mixture of frequencies, which activate separate neurons in the tonotopic auditory cortex. Nevertheless, we perceive this mixture as an integrated sound with unique acoustic properties. We used the Mismatch Negativity (MMN), a marker of auditory change detection, to determine whether individual harmonics are represented in sensory memory. The MMN elicited by duration and pitch deviations were compared for harmonic and pure tones. Controlled for acoustic differences between standards and deviants and their relative probabilities, the MMN was larger for harmonic than pure tones for duration but not for pitch deviance. Because the magnitude of the MMN reflects the number of concurrent changes in the acoustic input relative to a preexistent acoustic representation, these results suggest that duration is represented and compared separately for individual frequencies, whereas pitch comparison occurs after integration.