Friction stir welding is one of the newest methods of metal welding. The method is constantly being developed and friction stir spot welding (FSSW) is one of its varieties. The method is mainly used in the aircraft, automotive and shipbuilding industries. During the process, heat is generated as a result of friction between the tool and materials as well as plastic deformation of the joined materials. The paper presents a numerical analysis of welded structures made of 6061-T6 aluminium alloy. The specimens were joined by refill FSSW. This method joins metals in a solid state. The numerical calculations were performed using the ADINA System based on the finite element method. The sheets were modelled with shell elements and the joints were modelled with 3D-solid elements. The experimental investigations were carried out using a non-contact system allowing for measuring displacements and strains in real time. The numerical results were compared with the test ones. The structures were assessed regarding strength and the possibility of their application in the aircraft industry.