Abstract: The nucleation of three-dimentional Ge islands formed on a pre-patterned Si substrate with an array of round pits is studied. It is found that the Ge islands nucleate within pits with pointed bottoms and along the perimeters of pits with flat bottoms. This effect is determined by the difference between the distributions of elastic strains at the Ge/Si interface for differently shaped pit bottoms. The results of the simulation of growth show that, in the case of pits with pointed bottoms, the most relaxed regions are at the centers of the pit bottoms and the nucleation of islands takes place just in these regions. At the same time, in the case of pits with flat bottoms, the most relaxed regions are shifted from the pit bottoms to the pit edges, resulting in the nucleation of islands along the pit perimeters.