The heating distribution assessment on similar and dissimilar friction stir welded joints in AA6082 and AA5754 aluminium alloy sheets was investigated. The FSW experiments were carried out using constant rotational and welding speeds of 1500 rpm and 60 mm/min, respectively. Temperature was locally measured by means of K-type thermocouples inserted into thin grooves located on the bottom side of the sheets, in fixed positions, very close to the welding line. It was observed that the mechanical properties of joints are related to the heat distribution. In order to obtain a completely non intrusive temperature monitoring, that was able to follow the process dynamic, a non-contact measurement system based on infrared thermography was also developed. Such system, used for the experimental evaluation of temperature on the upper surface of the joints, is also able to detect the presence of flow defects with a non-destructive method, demonstrating its effectiveness as a diagnostic instrument for the on-line quality control of welded joints.