In this paper, the structural behavior of Hagia Sophia was analyzed by use of vibration records of the structure. The vibration records were measured by the micro tremor meters. The recorded data was utilized not only to define the mode shape but also to evaluate the structural problems. Firstly, the vibration characteristics of the main building were analyzed by combining the vibration records. Secondary, the deformation characteristics and the structural functions of the second cornice were investigated in the same manner as the main building. In case of main building, from the frequency domain analyses, the natural frequency of the main building was analyzed and the obtained natural frequencies were compared with the results of the previous researches. The vibration modes were investigated as well. From these results, the characteristics of the total structure were clarified and the structural problems were detected. In case of the second cornice, the base at the corner where was the junction of the main pier and the sub-dome connecting to the semi-dome showed the movement of the embedded stone. To investigate such phenomena, the same non destructive measurements were applied. Then, applying the finite element method to solve such structures, the structural behaviors were clarified and the health monitoring was performed.