Evaluation of damage of structures after large earthquake is an important task for health assessment. Vibrations of buildings give us valuable information on it. Among the representative structural characteristics, natural frequencies provide the global information. However they are relatively simple, accurate to measure and easy to obtain. Besides, the changes in frequencies must be considered to identify a damage of structures. This study will consider the frequencies and mode shapes shifts with various levels of seismic excitations. The excitations are represented by different intensity levels of the 1995 Hyogoken Nanbu Earthquake that are obtained in JR - Takatori Station. The acceleration data of E- Defense tests on full scale 4-story steel building will be analyzed. These will allow us detecting and localizing structural damage as well as evaluating the structural performances. The changes in frequencies and mode shapes are achieved from multi-input multi-output (MIMO) models. Those will be compared so as to get the results with reasonable accuracy. The aim of this paper is to propose a damage identification method in order to give correlation between the models and real damage of a steel building using real-size shake table tests.