Friction stir welding (FSW) was initially developed for welding aluminium alloys which were difficult to weld using conventional welding techniques. With the remarkable success accomplished with these alloys, materials manufacturers were passionate about using FSW with other materials. In the case of polymeric materials, the application of conventional FSW was not satisfactory due to the differences between the characteristics of metals and polymeric materials. Consequently, many modifications were developed to overcome the drawbacks of conventional FSW technique. For instance, heating the tool with an external heating source is one of the major modifications. The aim of this work is to clarify the quality of friction stir welding of polycarbonate (PC) in square butt configuration as a function of tool temperature, rotational speed and welding speed. This material was selected due to its transparency as well as its good photoelastic properties. Therefore, the defects can be easily detected and the residual stresses can be revealed under a polarized optical microscope. Four values of suggested welding parameters (pin temperature, rotational speed and welding speed) were investigated. Both the mechanical properties and the defect formation were studied in order to achieve a better welding joint. The investigation of samples macrostructure showed that several defects such as islands of melted and nonmelted material, discontinuous bonding line, macro-cracks, tunnels, flash formation, surface grooves, voids and root defects were formed as a response to the different interactions between the welding parameters. These defects can be minimized when the welding process is performed at a rotational speed of 1800 rpm, welding speed of 30 mm/min and tool temperature of 50 • C. In this situation, the joint efficiency of the welded joint reached 92.2% relative to the base material flexural strength.