Actually, one dimensional approaches are the most used site response analysis (SRA) in the Geotechnical Earthquake Engineering Practice, mainly due to the possibility of considering in a relative easy way, the nonlinear soil response. Nevertheless, these analyses are done in the frequency domain, so an unknown number of iterations are required according to the lineal equivalent method which does not account for any structural system or perform dynamic soil-structure interaction. Finite and different element methods are specifically suitable to generate analysis with the advantage of incorporating nonlinear subsoil behavior using ad hoc constitutive relations. Additionally, these methods enable the input of any structural system (e.g. tunnels, bridges, buildings, etc.) resulting in a coupled dynamic soil-structure interaction. In this paper, a comparison between the SRA results between different dimensional approaches (1D, 2D and 3D) is made using some of the most popular geotechnical software packages in FEM/DEM analyses, their results are calibrated and compared (in the free field case) with the 1D SRA results using synthetic seismograms. Finally, some recommendations and suggested practices include: boundary conditions (rigid and complaint in the base and absorbent in the lateral boundary) and input seismic accelerogram (in terms of accelerations or velocities, base line correction, etc.).