Using magnetoencephalography (MEG), we investigated the influence of long term musical training on the processing of partly imagined tone patterns (imagery condition) compared to the same perceived patterns (perceptual condition). The magnetic counterpart of the mismatch negativity (MMNm) was recorded and compared between musicians and non-musicians in order to assess the effect of musical training on the detection of deviants to tone patterns. The results indicated a clear MMNm in the perceptual condition as well as in a simple pitch oddball (control) condition in both groups. However, there was no significant mismatch response in either group in the imagery condition despite above chance behavioral performance in the task of detecting deviant tones. The latency and the laterality of the MMNm in the perceptual condition differed significantly between groups, with an earlier MMNm in musicians, especially in the left hemisphere. In contrast the MMNm amplitudes did not differ significantly between groups. The behavioral results revealed a clear effect of long-term musical training in both experimental conditions. The obtained results represent new evidence that the processing of tone patterns is faster and more strongly lateralized in musically trained subjects, which is consistent with other findings in different paradigms of enhanced auditory neural system functioning due to long-term musical training.