This paper investigates the importance of seismic soil-structure interaction in three-dimensional lined tunnels, assuming inelastic material behavior for both the concrete liner and the soft rock type of soil. The seismic response of the soil-structure system is obtained by the finite element method in the time domain. Viscous absorbing boundaries are used in conjunction with the discretization of the rock medium. Both the rock medium and the concrete liner are assumed to behave inelastically on the basis of the continuum damage mechanics theory. The seismic waves are assumed to have any arbitrary time variation and direction of propagation. The system is analysed with and without soil-structure interaction in order to assess its importance on the response of the system.