Missing dimer vacancies are always present on the clean Si(001) surface. The vacancy density can be increased by ion bombardment (Xe+, Ar+), etching (O2, Br2, I2, etc.) or Ni contamination. The equilibrium shape at low vacancy concentrations (<0.2¿0.3 monolayers) of these vacancy islands is elongated in a direction perpendicular to the dimer rows of the upper terrace, whereas for higher vacancy concentrations the equilibrium shape is rotated by 90°. The absence of dimerisation within the narrow vacancy islands at low vacancy concentration alone is not sufficient to explain this shape transformation, therefore it is suggested that the specific rebonding of these structures also plays a role. A more detailed analysis of the annealing behaviour, width, spacing between and depth of the elongated low-vacancy concentration vacancy islands reveals that the Ni-induced vacancy islands differ significantly from the etching-induced vacancy islands.