Germanium grows on pure Si(100)-(2×1) in the Stranski-Krastanov mode. Layer-by-layer growth is found for coverages below 3 ML before the onset of 3D islanding. In this regime the morphology of the Ge layer is strongly influenced by the misfit of 4.2% between layer and substrate. Around 1 ML aligned missing dimer defects are created which form a semiperiodic (2×12) arrangement. With increasing coverage this periodicity is gradually compressed and reaches a (2×8) reconstruction around 2.3 ML. This behaviour is discussed in terms of partial relaxation of the local strain. When further Ge layers grow on this (2xN) arrangement, only part of the missing-dimer defects of the lower layer are buried and a network of trenches partly reaching down to the substrate remains. Layer-by-layer growth up to higher coverage can be obtained using As as a “surfactant” during growth. Under these conditions no (2×8)-like arrangement is found. Up to 12 ML Ge coverage the layer grows free of defects forming extremely anisotropic Ge islands. At higher coverage a network of trenches arises which decorate an array of V-shaped defects previously found with TEM. The arrangement and the start of the overgrowth of these defects is studied.