Neural correlates of the processing of musical syntax-like structures have been investigated via expectancy violation due to musically unrelated (i.e., unexpected) events in musical contexts. Previous studies reported the implication of inferior frontal cortex in musical structure processing. However - due to the strong musical manipulations - activations might be explained by sensory deviance detection or repetition priming. Our present study investigated neural correlates of musical structure processing with subtle musical violations in a musical priming paradigm. Instrumental and sung sequences ended on related and less-related musical targets. The material controlled sensory priming components, and differences in target processing required listeners' knowledge on musical structures. Participants were scanned with functional Magnetic Resonance Imaging (fMRI) while performing speeded phoneme and timbre identification judgments on the targets. Behavioral results acquired in the scanner replicated the facilitation effect of related over less-related targets. The blood oxygen level-dependent (BOLD) signal linked to target processing revealed activation of right inferior frontal areas (i.e., inferior frontal gyrus, frontal operculum, anterior insula) that was stronger for less-related than for related targets, and this was independent of the material carrying the musical structures. This outcome points to the implication of inferior frontal cortex in the processing of syntactic relations also for musical material and to its role in the processing and integration of sequential information over time. In addition to inferior frontal activation, increased activation was observed in orbital gyrus, temporal areas (anterior superior temporal gyrus, posterior superior temporal gyrus and sulcus, posterior middle temporal gyrus) and supramarginal gyrus.