In order to enhance the opto-electronic properties of Ge dots embedded in Si a precise control of their structural properties is required. In this study, we have investigated the initial stages during the process of overgrowth by in situ scanning tunnelling microscopy and X-ray diffractometry. It is found that Ge dome clusters transform back into hut clusters after the deposition of 5 monolayers (ML) of Si at high temperature, while they preserve their shape at low overgrowth temperature. In addition, after the deposition of 3 ML of Si at low temperature, new clusters can be found with rectangular bases rotated by 45degrees compared to hut clusters. The changes in shape are accompanied by local changes in the strain and composition of the dots. The presented data give detailed insights into the shape and composition of Ge quantum dots before and after they have been overgrown with Si. (C) 2003 Elsevier B.V. All rights reserved.