We estimated the distribution of site response for ground motions in a period range of 2 to 4 s in the Kanto basin for earthquake resistant design of skyscrapers or base-isolated buildings with the resonant period. We used the spectral inversion method to separate source, path, and site effects by using the data from very dense seismic observation networks in the Kanto basin. The resultant site response was in good agreement with spectral ratio of records observed at ground surface and seismic basement. This indicates the estimation was successful. The resultant site response was large around Ichikawa city due to thick soft surface layers. In the east of Kanagawa prefecture, the site response showed variability from a factor of 3 to 5. The difference was not only due to the effect of 1-D velocity structure beneath the sites but also that of 3-D velocity structure.