In this study, AA 6063 (AlMgSi0.5) Aluminum alloy plates were welded by a solid state welding procedure, friction stir welding (FSW). The influence of pin structure on the microstructure of the weld region and the mechanical properties of the joints were studied. It has been seen that the helical structure on pinscrew has an effective role on the formation of a zigzag line in the weld region. While rather long and uninterrupted zigzag lines in the weld region are obtained when right helical pinscrew is used, left helical pinscrew gave rise to shorter zigzag lines. While the zigzag line has no effect on the mechanical properties of the as-welded joint, heat treatment after the welding (PWHT) procedure seriously affects the strength of the joint due to the zigzag line formed in the weld region. The mechanical strength decreases with right helical pinscrew in PWHT, whereas, left helical pinscrew causes an increase in mechanical strength.