The N1m component of the auditory evoked magnetic field in response to tones and complex sounds was examined in order to clarify whether the tonotopic representation in the human secondary auditory cortex is based on perceived pitch or the physical frequency spectrum of the sound. The investigated stimulus parameters were the fundamental frequencies (F0 = 250, 500 and 1000 Hz), the spectral composition of the higher harmonics of the missing fundamental sounds (2nd to 5th, 6th to 9th and 10th to 13th harmonic) and the frequencies of pure tones corresponding to F0 and to the lowest component of each complex sound. Tonotopic gradients showed that high frequencies were more medially located than low frequencies for the pure tones and for the centre frequency of the complex tones. Furthermore, in the superior–inferior direction, the tonotopic gradients were different between pure tones and complex sounds. The results were interpreted as reflecting different processing in the auditory cortex for pure tones and complex sounds. This hypothesis was supported by the result of evoked responses to complex sounds having longer latencies. A more pronounced tonotopic representation in the right hemisphere gave evidence for right hemispheric dominance in spectral processing.