The Friction Stir Welding (FSW) is a dynamically developing version of the pressure welding processes. High-quality welded joints can be created using this process for different engineering applications (e. g. automotive parts). Nowadays, the knowing of the properties and the behaviour of the welded joints is an important direction of the investigations, especially under cyclic loading. The research work aimed to demonstrate the behaviour of the friction stir welded joints under cyclic loading conditions. Fatigue Crack Propagation (FCG) experiments were performed on 5754-H22 and 6082-T6 aluminium alloys and their friction stir welded joints. The CT type specimens were cut parallel and perpendicular to the characteristic directions of the base materials and the welded joints, and the notch locations in the specimens of welded joints were different, too. Therefore, the propagating cracks represent the possible directions of the fatigue cracks both on the base materials and on the welded joints. The results of the fatigue crack propagation tests on the welded joints clearly demonstrate the different characteristics of the thermo-mechanically affected zone (TMAZ), the heat affected zone (HAZ), and the advancing (AS) and retreating sides (RS) of the weld nugget (WN). The investigations and their results were compared with each other and with the results can be found in the literature.