Abstract A boundary element formulation having nonlocal boundary conditions is presented for the dynamic analysis of a body with two regions. Nonlocal boundary conditions, used in the formulation, make it possible to analyze a body with three regions. The formulation is performed in Fourier transform space by using a constant element model. Based on the formulation presented in this study, two general purpose computer programs are developed for two and three dimensional elastodynamic problems. The programs perform the analysis in Fourier transform space and can also be used for static analysis by assigning a small value to the frequency. The results of some dynamic soil-structure interaction problems obtained using the programs are compared with those in the literature.