The creation of crystal defects during epitaxial growth, and their proper characterization and classification are among the most critical issues impacting epitaxial structures and device applications. Epitaxial layers of different SiGe composition grown by molecular beam epitaxy (MBE) on Si(001) and Ge(001) substrates have been studied by Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). The volumetric and surface structure of crystal defects revealed and characterized by TEM and AFM provided a detailed understanding of the major processes associated with defect creation and structural transformation during epitaxial growth. The main structural features were identified and correlations were made between crystal perfection and epitaxial growth conditions as also revealed by X-ray diffraction. (C) 2012 Elsevier B.V. All rights reserved.