During the last decade, friction stir welding has various applications in the automotive, shipbuilding, and aerospace industry due to its versatility. More recently, there have been trials to combine FSW with ceramic nanoparticle reinforcement in order to form MMCs locally on the weld line. This combination could result to potential applications on the above industries. In the present study, optical and electron microscopy, as well as microhardness and tensile testing, were used in order to determine the effect that SiC and TiC nanopowders have on the weld nugget of AA6082-T6 butt welds. It is the first time that such a thorough study via TEM in combination with EDS was conducted for this alloy. Emphasis was given on the distribution of dislocations and on the presence of the intermetallic and reinforcing particles in the weld. It was found that the grain size of all the specimens was dramatically decreased due to the dynamic recrystallization phenomenon. This also provoked the dilution of a lot of the intermetallic particles of the base metal and the multiplication of the dislocations. Between the two reinforced specimens, the SiC presented higher elongation while the TiC presented higher microhardness.