Positron annihilation spectroscopy is employed to investigate the density of defects in samples of aluminium alloys (2017 A and 6013) welded using the Friction Stir Welding method. The vacancy and dislocation densities were determined at the weld junction as a function of various parameters and conditions: Travel and rotational speed of welding tool, cooling of the surface of the welded material and the compositions of the welded alloys. The 3-state trapping model used in the computer analysis allowed to separate a vacancy component from a component related to dislocations. The determined lifetime of positron trapped by dislocation was much shorter than its experimental values referred to in literature, however, it is closer to the theoretical predictions.