The effect of processing parameters on mechanical and microstructural properties of dissimilar AA6082-AA2024 joints produced by Friction Stir Welding was analysed in the present study. Different samples were produced by employing a fixed rotating speeds of 1600 RPM and by using the advancing speeds of the tool of 80 and 115 mm/min. All the welds were produced in direction perpendicular to the rolling one for both the alloys and by changing, for all the processing conditions, the alloy positioned on the advancing side of the tool. The mechanical properties of the joints were evaluated by room temperature tensile tests. Fatigue tests on the welds were carried out by using a resonant electro-mechanical testing machine under constant loading control up to 250 Hz sine wave loading. The fatigue tests were conducted in the axial total stress-amplitude control mode with R=smin/smax=0.1. The microstructural evolution of the material was analysed by optical observations of the welds cross sections and SEM observations of the fracture surfaces.