A 6061-T6 aluminum alloy was self-reacting friction stir welded by using the specially designed tool with unequal shoulder diameters at a constant welding speed of 150 mm/min to investigate the effect of rotation speed on microstructure and mechanical properties of the joints. Excessive flash on the bottom surface of the joint and groove defects on both surfaces of the joint were formed when the lower shoulder diameter was much smaller. The suitable shoulder sizes were determined as 16 and 18 mm in lower shoulder diameter and upper shoulder diameter, respectively. The grain size and the dislocation density in the weld nugget zone (WNZ) increased with increasing rotation speed. The tensile strength of joints first increased with increasing rotating speed and then decreased remarkably as a result of the formation of void defect. The joints welded at lower rotation speeds were fractured in the thermal mechanically affected zone (TMAZ). However, the fracture locations of the defect-free joints were changed to the heat affected zone (HAZ) at higher rotation speeds.