Three-dimensional numerical simulations are carried out to investigate residual stresses generated by Friction Stir Welding (FSW). The modelling is carried out using two finite element commercial codes for greatest efficiency (SYSWELD and MARC). A thermal-mechanical transient state is used for the calculations. The thermal stage of the process is simulated by using two different numerical heat sources (a 2D and a 3D source, one with each code). Those numerical heat inputs are calibrated with the help of experimental results obtained by thermocouples and infra-red cameras. For the mechanical stage, the detailed tooling geometry, the lateral force from the tool onto the work-piece and the mechanical stir process are not simulated. But the mechanical characteristics of all the re-crystallised materials involved are determined notably by micro-tensile tests and then used in the calculations. Finally, experimental measurements of FSW residual stresses made by neutrons diffraction are compared with the numerical residual stresses from both codes.