Because of the repeated earthquake and the problem such as the aging of buildings, a number of studies of Structural Health Monitoring (SHM) is have been done. Now, the writer is developing structural health assessment system for steel and reinforced concrete structures aiming for completion in 2014. In this system, following three programs for automatically estimating the physical quantity that is important for assessing the integrity of the structure are planned. First program is what automatically estimate the modal parameters (natural frequency and damping ratio) of the structure by the time history by using the subspace method. Second program is what automatically estimate the inter-layer parameters (stiffness and damping coefficient) by the time history by using the adaptive Kalman filter. Third program is what automatically estimate the story drift angle by time history by using the adaptive Kalman filter. The proposed method is expected to be estimated in consideration of the higher order modes than the conventional method by reverse modal analysis.