Soil-structure interaction (SSI) analysis is generally a required step in the calculation of seismic demands in nuclear structures, and is currently performed using linear methods in the frequency domain. Such methods should result in accurate predictions of response for low-intensity shaking, but their adequacy for extreme shaking that results in highly nonlinear soil, structure or foundation response is unproven. Nonlinear (time-domain) SSI analysis can be employed for these cases, but is rarely performed due to a lack of experience on the part of analysts, engineers and regulators. A nonlinear, time-domain SSI analysis procedure using a commercial finite-element code is described in the paper. It is benchmarked against the frequency-domain code, SASSI, for linear SSI analysis and low intensity earthquake shaking. Nonlinear analysis using the time-domain finite-element code, LS-DYNA, is described and results are compared with those from equivalent-linear analysis in SASSI for high intensity shaking. The equivalent-linear and nonlinear responses are significantly different. For intense shaking, the nonlinear effects , including gapping, sliding and uplift, are greatest in the immediate vicinity of the soil-structure boundary, and these cannot be captured using equivalent-linear techniques.