To determine seismic ground motion for aseismic design, it is necessary to take site effects into account, such as non-linearity of soil and geological irregularities. In this paper, we discuss two aspects of site effects. One is the estimation of nonlinear earthquake response of soil deposits, and the other the estimation of seismic motion on the ground that has topographical and geological irregularities. We propose a new stress-strain model that is applicable to earthquake response analyses of soil deposits under large earthquakes. Next, we develop a practical method to evaluate amplification characteristics of ground motion on the irregularly layered ground.