A full scale five-story reinforced concrete building was built and tested on the NEES-UCSD shake table. The purpose of this experimental program was to study the response of the structure and nonstructural systems and components (NCSs) and their dynamic interaction during seismic excitation of different intensities. The building specimen was tested under base-isolated and fixed-based conditions. In the fixed-based configuration the building was subjected to a sequence of earthquake motion tests designed to progressively damage the structure. Before and after each seismic test, ambient vibration data were recorded and additionally, low amplitude white noise base excitation tests were conducted at key stages during the test protocol. A quasi-linear response of the building can be assumed due to the low intensity of the excitation and consequently modal parameters might change due to the structural and nonstructural damage. Using the vibration data recorded by 72 accelerometers, three system identification methods, including two output-only (SSI-DATA and NExT-ERA) and one input-output (DSI), are used to estimate the modal properties of the fixed-base structure at different levels of structural and nonstructural damage. Results allow comparison of the identified modal parameters obtained by different methods as well as the performance of these methods and studying the effect of the structural and nonstructural damage on the dynamic parameters. The results show that the modal properties obtained by different methods are in good agreement and that the effect of structural/nonstructural damage is clearly evidenced via the changes induced on the estimated modal parameters of the building.