Joint experimental and theoretical study of Ge nanoislands growth on pit-patterned Si substrate is carried out. Si(0 0 1) and Si(1 1 1) substrates, that have been templated by means of electron beam lithography and reactive ion etching, were used to grow Ge by molecular-beam epitaxy. Atomic-force-microscopy studies showed that, at certain conditions of Ge growth on the Si(0 0 1) and Si(1 1 1) pit-patterned substrates, Ge nanoislands are formed at the pits' edges and inside the pits, respectively. The effect is interpreted in terms of energy surfaces mapped out through molecular dynamics simulations of pit-patterned surface. (C) 2010 Elsevier B.V. All rights reserved.