The Friction stir welded joints on structural aluminium and magnesium alloys, made by using a universal milling machine with rotation speed to travel speed ratio between 3 and 16 rev/mm, have presented very good quality and mechanical properties compared to the welded joints by conventional processes like GMAW. Tensile strength of FSWed Aluminium alloy 6261-T6 rise to 84% of that of the parent metal; while for FSWed magnesium alloy AZ31B, the tensile strength rise to 85% of the base metal. The general microstructure is composed of equiaxed fine grains resultant from the dynamic recrystallization phenomena produced during the welding process. Microhardness tests have shown higher values in the nugget zone than in the base metal, but with typical variations for this type of materials. However, the welded specimen showed a failure zone in the limit of the welds , where planes of weakness are presented due to the accumulation of oxides or the presence of microtextures non favourable to the plastic deformation during tensile tests.