Japan is one of the most advanced countries in earthquake technology. Isolation systems are widely used in large-scale structures such as hospitals and communication centers. For example, an isolated office building has been used as a hub of recovery from accident by Great East Japan Earthquake in Fukushima nuclear power plant. In the meantime, application of probabilistic risk assessment is used for structure of nuclear power plants. In 2006, Regulatory Guide for Reviewing Seismic Design was revised and according to guideline, it is necessary to consider the residual risk1. In addition, seismic isolation systems are expected to be used for nuclear power plants. Recently, the risk of isolation system’s failure needs to be assessed in case of large ground motion. This paper deals with probabilistic approach on seismic response of an isolated structure. Consequently, sensitivity analysis is carried out. Then, as nonlinear behavior in rubber bearings occurs during huge earthquake, it has to be considered in the sensitivity analysis.