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Conservation techniques within the framework of structural health monitoring, particularly through dynamic measurements and operational modal analysis, are becoming popular for condition-based maintenance and decision-making in historic structures. Nonetheless, while effective for giving insight into the overall behaviour of structures, these techniques may fail at detecting local damages with limited effects on the modal features of the system. In this regard, the analysis of propagating waves throughout the structure poses an attractive alternative for data-driven damage identification. Specifically, some encouraging results have been reported on the application of seismic interferometry to reinforced concrete structures, albeit the number of works concerning ambient vibrations is far scarce, and practically nonexistent in the realm of historic structures. In this light, this article explores the synergistic application of operational modal analysis and ambient noise deconvolution interferometry for the structural identification of historic structures through three different case studies, namely the Sciri Tower in Perugia, the Consoli Palace in Gubbio and the bell-tower of the Basilica of San Pietro in Perugia. The first case study represents a typical example of a masonry tower inserted into a building aggregate, while the second one constitutes a particular case of a monumental masonry palace. The presented results and discussion cover diverse aspects of the identification of wave velocities, signal processing strategies, effects of dispersion and robustness of the identification. Finally, the case study of the bell-tower of the Basilica of San Pietro illustrates the application of operational modal analysis and deconvolution interferometry for damage identification. To do so, two different ambient vibration tests conducted before and after the 2016 Central Italy seismic sequence are studied. The results show concentrated reductions in the wave velocities in the area of the belfry, which demonstrates that deconvolution interferometry constitutes a complementary technique to operational modal analysis for damage localization and, to some extent, damage quantification.