Magnetoencephalographic correlates of rapid emotional responses (50–80 ms) in frontal and occipito-temporal regions have recently been reported using a novel MultiCS Conditioning paradigm with odor-conditioned faces. As those short-latency responses were supposed to partially reflect initial access to nonextinguished emotional memories, it could be predicted that they outlast the extinction phase. To test this hypothesis, appetitively and aversively odor-conditioned faces were frequently presented during extinction while event-related magnetic fields were recorded. Affect-specific responses in frontal and occipito-temporal areas were found in the early (50–80 ms) but not in the later (130–190 ms) time interval following extinction learning. These results suggest that previously acquired emotional memories can be accessed at initial processing stages but become ineffective in modulating processing at later stages as extinction proceeds.