This chapter investigates on the characterization of friction stir welded dissimilar aluminium alloys AA2024 with AA5052, AA2024 with AA6061 and AA 5052 with AA6061. Five tool designs were employed with first two dissimilar combinations to analyze the influence of rotation and traverse speed over microstructural and mechanical properties. H13 tool steel was used as tool material with various pin profiles which includes cylindrical, cylindrical-threaded, squared, tapered and stepped types. In the dissimilar welding of AA 2024 with AA 5052, sound welds were produced with stepped pin tool. In the dissimilar welding of AA 2024 with AA 6061, ratio between tool shoulder to diameter of tool pin was the most influential factor. Welded joints failed in the Heat affected zone (HAZ) of 6061 where the hardness values were comparatively less. In dissimilar welding of AA 5052 with AA6061, cylindrical pin tool was used at a constant speed of 710 rpm and at different feed rates of 28 and 40 mm/min. Micro structural examination showed variation of grain size in every zone and their influence on mechanical properties. Correlating mechanical and metallurgical properties, the optimized process parameters of speed and feed were identified to be 710 rpm and 28 mm/min respectively for all attempted dissimilar combinations.