This study investigates the effects of prescribed damage on the walls of masonry buildings by experimental and numerical methods. Ambient vibration survey method was applied to an existing, two-story, unreinforced masonry building to determine its dynamic characteristics, such as mode shapes and natural frequencies. Then, the walls on two exterior sides of the building were demolished, and dynamic testing was repeated for the damaged building. As the next step, the amount of damage on the building was increased by more impacts, and the dynamic characteristics of the heavily damaged building were identified. The results obtained from the undamaged, damaged and heavily damaged building were compared, and the damage effect on the natural frequencies of the building was noted. Besides, finite element analyses of the undamaged, damaged and heavily damaged buildings were performed. It was found that, the numerical models, constructed with code-based material properties, do not sufficiently represent the dynamic behavior of masonry buildings. Secondly, as the result of the sustained damage, while the experimental and the numerical modal analyses revealed the decrease in the dominant frequencies of the building, the difference between them increases with the severity of the damage. With the framework presented in this study, the behavior of masonry buildings can better be determined and used for analysis purposes.