The aim of present research was to study the effect of the position of the tool relative to the support backing plate of the FSW machine on the formation of defects and on alterations of the microstructure and mechanical properties of friction stir welds in phosphorus-deoxidised copper (Cu-DHP) thin sheets of 1 mm thick. The welds were carried out using position control conditions; distances between the tool and the backing plate of 0.1 mm, 0.075 mm and 0.05 mm were used. The formation of defects like continuous voids along the weld is very influenced by the tool position, though the heat-input plays an important role in the process. Large grain refinement was observed in the nugget of the welds; the change of the relative tool position has little effect on this grain refinement. Substantial hardening was observed in the thermomechanically affected zone (TMAZ) of the welds. The welds exempt of defects, such as continuous voids, attained a little tensile strength overmatch condition.