Further improvement of phase change memory devices based on Ge–Sb–Te alloys imposes the reduction of the active cell dimensions to the nanoscale. We investigate the atomic arrangement of Ge1Sb2Te4 and Ge2Sb2Te5 nanowires. We identify the stacking sequence in each crystal structure by combining the direct observation by High Angle Annular Dark Field imaging and proper simulations. We find out that Ge and Sb atoms randomly share the same lattice sites, although this configuration is considered not stable according to the existing theoretical models elaborated for the bulk material.