Friction stir welding of AA5456 aluminum alloy in lap joint configuration is with two different tempers, T321 and O, and different thicknesses, 5mm and 2.5mm was investigated. The influences of tool geometry and various rotational speeds on macrostructure, microstructure and joint strength are presented. Specifically, four different tool pin profiles (a conical thread pin, a cylindrical-conical thread pin, a stepped conical thread pin and Flared Triflute pin tool) and two rotational speeds, 600 and 800 rpm, were used. The results indicated that, tool geometry influences significantly material flow in the nugget zone and accordingly control the weld mechanical properties. Of particular interest is the stepped conical threaded pin, which is introduced for the first time in the present investigation. Scanning electron microscopy investigation of the fracture location of samples was carried out and the findings correlated with tool geometry features and their influences on material flow and tension test results. The optimum microstructure and mechanical properties were obtained for the joints produced with the stepped conical thread pin profile and rotational speed of 600 rpm. The characteristics of the nugget zone microstructure, hooking height, and fracture location of the weld joints were used as criteria to quantify the influence of processing conditions on joint performance and integrity. The results are interpreted in the framework of physical metallurgy properties and compared with published literature.