Abstract: A method for creation of Ge/Si structures with space-arranged nanoislands by heteroepitaxy on the pre-patterned Si(001) substrates with a square grid of the etched pits is developed. The influence of depth and inter-pit spacing on the nucleation and growth of Ge(Si) nanoislands is studied. It is shown, that the nanoislands are formed either inside pits or at their periphery depending on the pit depth. It is found that the size of the nanoislands grown inside the pits goes up with the increase of the inter-pit distance from 1 to 4 μm. The pronounced photoluminescence signal related with the space-arranged arrays of quantum dots with a period of 1 μm is observed in the range of energies from 0.9 to 1.0 eV.