In conventional modeling of frame structures, soil-structure interaction is usually not taken into account. This leads to differences in the response of the structure. Base isolation is aimed at uncoupling the upper structure from the foundation, reducing thus the structural internal forces. For the last three decades, there have been done a lot of investigations to prove the effectiveness of baseisolation. The procedure for design and analysis of base isolated structures is usually based on the fixed base assumption where soil-structure interaction (SSI) effects are not considered. The presented investigations were aimed at analyzing the effects of SSI on base isolated frame structures. The influence of SSI on the structural response was shown by analysis of the results obtained for two models: the first model represented a base isolated frame structure, while the second model included the influence of the soil medium. In the presented investigations, three types of soil were taken into consideration, namely hard, medium and soft soils, as stated in Eurocode 8. The sub-soil conditions are represented by 30m thick soil deposits with four layers which rest on the bedrock. The side boundaries of the finite element model were composed of newly programmed infinite elements to eliminate the reflection of the seismic waves back to the model. The base isolated frame structure was supported by four high damping rubber bearings (HDRB). The lateral behavior of HDRB was considered as bilinear. The results from the performed 2D nonlinear dynamic analysis show that, in addition to the soil medium considered in the analysis, the structural properties and soil characteristics play a considerable role in seismic response of base isolated structures. Attention should be paid in case of base isolated structures founded in soft soil local conditions, because the flexibility of the soil can significantly increase the internal structural forces.