As for the application of the conventional soil-foundation-structure interaction analysis, rigorous seismic motion should be taken into consideration, in order to know the exact response of the system. It is qualita-tively known that the geological irregularities amplify the seismic motion, and the existence of foundation generates low-pass-filtered motion. To estimate those effects quantitatively, the following are studied. The former, characteristics of the amplified seismic motion, is analyzed by two-dimensional finite element method. The latter, the effective seismic motion of caisson foundation, is investigated by tree-dimensional wave propagation theory. Results of these studies are summarized and simplified for applying to seismic design.