The 2024 alloy (Al-Cu-Mg) is used for minimizing the weight of structural components in the transportation industry. However, this alloy is not easy to weld by traditional techniques. Friction stir welding (FSW) is a recently developed solid state process which removes the solidification defects. In this study, the microstructures of FSW welds of this alloy were finely characterized by SAXS, DSC, TEM, SEM, EBSD and optical microscopy. In order to highlight the interactions between deformation, precipitation and recrystallisation, which all take place during the welding of the 2024 alloy, model experiments were carried out as well as a comparative study between the alloys 5251 and 2024. The combination of the welding characterisation and the model experiments allow to define the metallurgical phenomena controlling the mechanical strength of the welded joints and their microstructure. In addition, a detailed characterisation of the mechanical behaviour of the welded joints was carried out, validated by a finite element model.