Background: The human auditory cortex automatically encodes acoustic input from the environment and differentiates regular sound patterns from deviant ones in order to identify important, irregular events. The Mismatch Negativity (MMN) response is a neuronal marker for the detection of sounds that are unexpected, based on the encoded regularities. It is also elicited by violations of more complex regularities and musical expertise has been shown to have an effect on the processing of complex regularities. Using magnetoencephalography (MEG), we investigated the MMN response to salient or less salient deviants by varying the standard probability (70%, 50% and 35%) of a pattern oddball paradigm. To study the effects of musical expertise in the encoding of the patterns, we compared the responses of a group of non-musicians to those of musicians. Results: We observed significant MMN in all conditions, including the least salient condition (35% standards), in response to violations of the predominant tone pattern for both groups. The amplitude of MMN from the right hemisphere was influenced by the standard probability. This effect was modulated by long-term musical training: standard probability changes influenced MMN amplitude in the group of non-musicians only. Conclusion: This study indicates that pattern violations are detected automatically, even if they are of very low salience, both in non-musicians and musicians, with salience having a stronger impact on processing in the right hemisphere of non-musicians. Long-term musical training influences this encoding, in that non-musicians benefit to a greater extent from a good signal-to-noise ratio (i.e. high probability of the standard pattern), while musicians are less dependent on the salience of an acoustic environment.