In April 2016, Kumamoto earthquake occurred in Japan and many wooden houses collapsed and many lives were lost because of the second and larger main shock. As a result, the need for Structural Health Monitoring (SHM) for wooden houses is receiving increased attention. In the SHM system, maximum inter-story drift angle is considered as the damage index. We assume that the first story of a wooden house will be damaged so that we need only to focus on the response of this first story. Hence, we install accelerometers on the ground floor and the second floor. In order to estimate the inter-story drift angle, we need to integrate the acceleration records twice. The simple double integration will result in erroneous results. Thus, in this paper, we propose the most appropriate integration method to estimate the maximum story drift angle with high accuracy using two accelerometers.