The defects of Ge quantum dot arrays formed at moderate temperatures on the Si(0 0 1) surface have been investigated by the ultra high vacuum scanning tunnelling microscope integrated with the molecular beam epitaxy chamber. A preliminary classification of the defects has been carried out. Morphological peculiarities of the defects have been studied. The surface densities of defects of different types have been determined. (C) 2009 Elsevier B.V. All rights reserved.