Seismic behavior and damage of historical masonry buildings significantly depends not only on materials and geometric properties, but also on structural detailing, modifications and condition over time. This produces the need for detailed safety assessments where both aleatory and epistemic uncertainties should be duly considered. In this respect, the type of floor and roof systems has major impact on seismic performance and vulnerability of masonry buildings. This study deals with the role of vaults in seismic response and damage of historical masonry buildings. After that an archetype building is selected, vaulted systems are implemented in the global structural model, which is developed according to the equivalent frame method (EFM). Pushover analysis results show that vault damage alters the overall capacity curve of the structure, reducing the maximum base shear capacity. Geometric factors, including the ratio of vault thickness to span length, are critical in determining collapse points. Understanding these aspects is essential for accurate damage assessment and effective strengthening strategies.