Studies using a brain index for pre-attentive change detection, the mismatch negativity (MMN), suggested distinct neuronal populations for signaling changes in sound duration and frequency. However, these studies used only durations within the temporal window of loudness summation (ca. 200 ms) in which any duration change is accompanied by a loudness change. Hence, the present study employed stimulus durations both beyond and within this temporal window in order to examine the genuine duration representation in the brain. Magnetic mismatch responses (MMNm) for duration and frequency changes were compared with each other. The equivalent current dipole (ECD) of the duration MMNm was located in the auditory cortex slightly posterior to that for the frequency MMNm irrespective of stimulus duration. The results suggested separate memory representations for sound duration and frequency in the human brain.