This paper is focused on the fatigue behaviour of aluminium alloy welded joints, which can represent regions of weakness in the ship structure. The traditional methods for fatigue assessment of welded joints have some limitations, and are extremely time consuming. In order to overcome these difficulties, the Risitano’s method, based on thermographic analysis, have been applied to predict the fatigue behaviour of welds. Experimental tests have been carried out to assess and compare the high-cycle endurance limits of different welded joints, obtained by means of Friction Stir Welding (FSW) and MIG techniques. The results obtained resorting to the Thermographic Method (TM) show a good agreement with those derived from the experimental data, represented through S-N curves.