The selective epitaxial growth of germanium on nano-structured periodic silicon pillars and bars with 360 nm periodicity on Si(001) substrate is studied to evaluate the applicability of nano-heteroepitaxy on the Ge-Si system for different fields of application. It is found that SiO2 used as masking material plays the key role to influence the strain situation in the Si nano-islands. To analyze this in detail, X-ray diffraction techniques in combination with theoretical simulations based on the kinematical X-ray scattering from laterally strained nano-structures and finite element method (FEM) calculations of the strain field are applied. The oxide related strain in the Si scales about linearly with the thickness of the SiO2 mask, but FEM simulations supposing a homogeneous stress distribution in the oxide are not sufficient to describe the local strain distribution in the nano-structures. It is demonstrated that the Ge lattice relaxes completely during growth on the Si nano-islands by generation of misfit dislocations at the interface, but a high structural quality of Ge can be achieved by suited growth conditions. (C) 2011 Elsevier B.V. All rights reserved.