The analysis of seismic wave propagation and amplification in complex geological structures raises the need for efficient and accurate numerical methods. The solution of the elastodynamic equations using boundary element methods (BEMs) gives rise to fully-populated matrix equations. Earlier investigations on the elastodynamic equations have established that the Fast Multipole (FM) method reduces the complexity of a BEM solution to N log N per GMRES iteration. The present Article addresses the extension of the FM-BEM strategy to 3D multi-domain elastodynamics in the frequency domain. Using this FM-accelerated BEM it is now possible to study the propagation of seismic waves in 3-D alluvial basins at a much lower cost than with standard BEM. Validations are performed for canonical basins and comparisons to previous works are proposed. It shows the efficiency and accuracy of the fast BEM formulation proposed.