The soil-structure interaction(SSI) effect should be considered to accurately assess the seismic response of structure constructed on soft soil site other than the hard bedrock. Recently, the demand of SSI analysis has increased due to strengthening of the regulatory guidelines of nuclear power plant such as the USNRC SRP 3.7.2. In this study an accuracy and running time of the KIESSI-3D program for large-scale 3D SSI analysis were investigated. The seismic SSI analysis using the KIESSI-3D program was performed for several examples of large-scale three-dimensional soil-structure interaction system. The analysis results were compared with those of the ACS/SASSI program. Good agreements in transfer functions at selected locations showd that KIESSI-3D yields accurate solution for large-scale SSI problem. Moreover, it was found that running speed of the KIESSI-3D for large-scale 3D SSI analysis is much faster than that of the ACS/SASSI about 30～2000 times.