The Friction Stir Welding (FSW) technique is a solid-state joining process usually applied to weld high strength aluminium alloys of the AA2XXX, 7XXX and 6XXX series, with applications in the aerospace, automotive, shipbuilding and marine construction industry. The main advantage of this technique, towards the more traditional welding systems, is a lower heat input with consequently more limited microstructural changes and higher mechanical characteristics of joints. The FSW process produces three zones with different microstructures in the joints: the nugget (N), the thermo-mechanically altered zone (TMAZ) and the heat altered zone (HAZ). Both plastic deformation and friction heat provoke microstructural variations that affect the mechanical characteristics of the different joint zones. These variations depend on the heat input which in turn is a function of welding parameters, such as rotational and advancing speed of the pin. After welding, also the corrosion resistance of the joint results modified with respect to that of the base material and numerous authors have investigated the corrosion behavior of FSW joints on various aluminium alloys. The results of these research studies are not always concordant. Some authors showed that the joints have a corrosion resistance higher than or equal to that of the base material. Other authors evidenced a preferential attack on either the nugget, or the nugget/TMAZ interface or the HAZ. The different results can be due to different parameters used in the welding, such as rotational and advancing speed. The aim of this paper is the investigation of the corrosion behavior of FSW AA2139-T3 and AA2198-T3 in 3.5% NaCl. Pitting potentials of different electrodes obtained from either N, or adjacent zone, containing TMAZ and HAZ, or base alloys were measured after 1h or 16h immersion in the aggressive solution. Short circuit currents of N/base alloy couples were also recorded. In the FSW joint of AA2139-T3, the pitting potential of N zone was higher than that of base alloy. In the N/base material couple, N was the cathode and stimulated the corrosion of adjacent base alloy. An opposite behavior was detected on the FSW joint of AA2198-T3. The joints were examined by optical microscope (OM) and scanning electron microscope (SEM). The distribution of the intermetallic particles and the microstructures of the two joints are not very different. So the opposite behavior of the joints can be rather ascribed to the different composition of the intermetallic particles, which are Cu- and Fe-rich in AA2198-T3 alloy, while they contain a AlCuFeMn intermetallic compound with lower cathodic activity in the AA2139-T3 alloy.