The method for estimation of foundation-input-motion based on ambient vibration tests is presented. In the proposed method, several theirs of construction are averaged to estimate foundation-input-motion. But, if we average them simply in frequency domain, we obtain foundation-input-motion which is affected by superstructure. We exclude affection of superstructure by using Fourier-spectral-ratio of top-floor’s per basement-floor’s. Relation between estimation precision and number of averaging samples are discussed. Base-isolated buildings have isolated-layer between basement and superstructure. Therefore, inertial force of superstructure doesn’t affect foundation-input-motion of earthquakes. By using earthquakes data of base-isolated buildings, we obtain foundation-input-motion which is not affected by superstructure.