The tool geometry is a crucial characteristic of the friction stir welding (FSW) process; its design is the key to the successful FSW application for a wide range of materials and thicknesses improving the weld strength and fatigue life. The present study investigates the influence of three shoulder geometries on the FSW joint performance, in terms of residual stresses state, microhardness profile and mechanical properties of 1.5 mm thick AA 6082-T6 FSW joints in the butt-joint configuration. The three tool geometries are characterized by three different shoulders: a shoulder with scroll, a shoulder with a shallow cavity, and a flat shoulder. Transverse and longitudinal tensile tests at room temperature were performed in order to evaluate the mechanical properties, respectively, of the joints and of the stirred zone, while the fatigue tests were performed transversally to the joint line.