A general numerical model for the analysis of soil motion due to high-speed train passage and effects on nearby surface and underground structures is presented in this paper. Soil, ballast and structures are represented using a three-dimensional time domain boundary element approach. Material damping has been included in the time domain formulation. Equilibrium and compatibility between soil and underground or surface structures is established in a rigorous manner in order to take into account soil–structure interaction. In contrast to other existing approaches, effects on a particular structure and the influence of non-uniform soil conditions along the track can be evaluated. Numerical results are obtained for different situations and some of them are compared with existing experimental records. The experimental values are to a large extent reproduced by the present numerical approach. Ballast influence and effects of high-speed train passage on a concrete underpass structure are analysed.