Friction stir welding (FSW) is a quite recent welding method which takes advantage of being performed in the solid state. Compared with the usual welding processes, it therefore presents many benefits such as a lower heat-input, a reduction of residual stresses and an elimination of the solidification defects etc.. Up to now, it has essentially been applied to aluminium alloys and far more recently to a small number of bimaterials. The present study deals with three kinds of beads between pure copper and a 6082 aluminium alloy. Both materials were butt joined by FSW. The welds differ by the location of the tool which was placed either at the interface between the two metals or on the copper or the 6082 side of this surface. Their structure was characterized at a multi-scale level by using a number of techniques. Tensile and microhardness tests were also performed. The tool place is shown to govern the microstructure and the ensuing mechanical behaviour of the weld. Its influence on the plastic flow with its repercussions on i) welding defects and ii) mechanical properties is going to be demonstrated. Some ways of improvement of the welding process will finally be suggested.