The purpose of this paper is to justify that it is necessary to take into account physical and mechanical properties of soil and different materials of erected structures for damping vibrations in dynamic loads, and to suggest tools for modelling the damping effect (natural or engineering induced) between foundation and soil. A technique is suggested for modelling the behavior of structure in time history analysis taking into account material damping. When solving this problem, the following results were obtained: the physical meaning of material damping was described; Rayleigh damping coefficients were computed through modal damping coefficients. Numerical analysis was carried out for the structure together with soil in earthquake load. Time history analysis was carried out for the problem. Peak values of displacement, speed and acceleration at the roof levels were compared. Analysis results were compared (with and without taking into account material damping). Significant influence of damping on the stress-strain state of the structure has been confirmed.