We analysed two different neural mechanisms related to the unconscious processing of auditory stimulation, neural adaptation and mismatch negativity (MMN), using magnetoencephalography in healthy non-musicians. Four kinds of conditioning stimulus (CS): white noise, a 675-Hz pure tone, and complex tones with six (CT6) and seven components (CT7), were used for analysing neural adaptation. The seven spectral components of CT7 were spaced by 1/7 octaves between 500 and 906 Hz on the logarithmic scale. The CT6 components contained the same spectral components as CT7, except for the center frequency, 675 kHz. Subjects could not distinguish CT6 from CT7 in a discrimination test. A test stimulus (TS), a 675-Hz tone, was presented after CS, and the effects of the presence of the same 675-Hz frequency in the CS on the magnetoencephalographic response elicited by TS was evaluated. The P2m component following CT7 was significantly smaller in current strength than that following CT6. The equivalent current dipole for P2m was located approximately 10 mm anterior to the preceding N1m. This result indicated that neural adaptation was taking place in the anterior part of the auditory cortex, even if the sound difference was subthreshold. By contrast, the magnetic counterpart of the MMN was not recorded when CT6 and CT7 were used as standard and deviant stimuli, respectively, being consistent with the discrimination test. In conclusion, neural adaptation is considered to be more sensitive than our consciousness or the MMN, or is caused by an independent mechanism.