This paper concerns the structural identification of historical masonry buildings with reference to a case study, which is discussed in detail. The building is located in Southern Italy (Lecce). It has an ancient vaulted roof that is complex and commonly found in old masonry structures. This study takes advantage of extensive historical and structural investigations of the building. Preliminary activities have been conducted to obtain information about the current state of the structure including the geometry, morphology, structural details, material properties, prior interventions, and existing damage. This process was supported by an historical investigation into the conceptual background and construction methods used to build the structure. After the historical investigation, a series of experiments, including dynamic tests, were conducted on a number of the vaults to determine their dynamic response characteristics under operational conditions. A numerical model was also determined. In this paper, the primary dynamic test results and modelling assumptions are reported. Comparisons between numerical and experimental results are discussed.