Digital music collections often contain different versions and interpretations of a single musical work. In view of music retrieval and browsing applications, one important task, also referred to as audio synchronization, is to automatically time-align two given audio recordings of the same underlying piece. In this paper, we present a novel synchronization procedure, which can compute meaningful audio alignments even in the presence of structural variations. Such variations include the omission of repetitions, the insertion of additional parts (soli, cadenzas), or differences in the number of stanzas in popular, folk, or art songs. As one main contribution, we introduce the concept of path-constrained similarity matrices. This enables us to employ a flexible and efficiently computable partial matching procedure in the optimization step of our synchronization algorithm. Our overall strategy aims at aligning preferably long consecutive runs while avoiding an over-fragmentation of the...