The objective of this study was to determine the effects of the tool pin diameter and tool rotation on the fatigue behaviour of friction stir welded (FSW) lap joints. FSW lap joints of AA 5754 aluminium alloy plates were produced by means of a conventional semiautomatic milling machine. Consequently, defect free FSW lap joints were produced on alloy plates at a constant traverse speed but with different tool pin diameter and tool rotation. Therefore, within this study, tool rotation and the tool pin diameter were accepted as variable parameters, while others held fixed. The results of the tests performed, indicate that an optimisation is required for the studied parameters, in order to obtain reasonable fatigue strength. An index, related to tool rotation, traverse speed, pin diameter, and pin height can be identified and used to select optimum parameters for FSW applications.