In the present study, friction stir welding (FSW) of butt and scarf joints of Al 6063-T6 were investigated. Five different tool pin profiles (cylindrical, tapered cylindrical, square, triangular, and hexagonal) were applied for performing welding. Scarf joint, being a new joint configuration, was used and effect of pin profiles was investigated on this type of joint configuration. The effect of pin profiles on microstructure, micro-hardness, impact and tensile properties of friction stir welded Al 6063-T6 was investigated. Scanning electron and optical microscopy were employed to characterize the different zones of welded joints. A thorough discussion on correlation between mechanical properties and microstructure has been made. In addition, the formation of various defects during the FSW was discussed with the help of fractography of the fractured surfaces.