A base isolation system placed within a structure for seismic protection will perform differently in the presence of soil-structure-interaction phenomena, as compared to the case where the structure is founded on competent soil and/or rock. This is so for two basic reasons: (a) there is filtering affecting the input ground motion signal at the base of the structure, and (b) the overall mechanical characteristics of the combined soil-structure system have changed as compared to the original structure resting on firm ground. Thus, a base isolation design has to account for soil-structure-interaction in order to have the system fine-tuned to the particular geological conditions and seismicity of the construction site in question. In this work, we introduce a distributed mass representation of the superstructure that has four possible dynamic response modes, namely flexure, shearing, torsion and axial vibrations. The foundation is treated as a rigid block, and the soil is represented by the equivalent spring-damper-virtual mass system, whereby these mechanical parameters may be frequency dependent. Typical base isolation systems used nowadays are lead rubber bearing designs whose mechanical behavior comprises a spring element, a damper and a hysteretic component. In terms of analysis, a substructuring methodology is employed that is cast in the frequency domain, with conditions of equilibrium and compatibility enforced at the common structure-foundation-soil boundaries. This approach is both efficient and adequate for investigating soil-structure-interaction effects, but cannot handle the hysteretic behavior of the base isolator, which is better captured by using time-stepping algorithms. In closing, some comments are made regarding possible ways for incorporating the base isolator in the present soil-structural system analysis, along with some preliminary results.