Nickel and copper were potentiostatically deposited onto monocrystalline n-Si (100) wafers and in nanoporous SiO2/Si template from 0.5 M NiSO4 + 0.5 M H3BO3 and 0.005 M CuSO4 + 0.5 M H3BO3 solutions. Nanoporous SiO2/Si template was formed by etching in dilute HF solution of ion tracks. The latter were produced by high-energy (380 MeV) Au+ ions bombardment of silicon oxide thermally grown on silicon (100) substrate. The deposition of metals was studied using cyclic voltammetry (CV), chronoamperometry; the structure and morphology of products were ex-situ investigated by SEM and XRD. The level of pores filling was controlled by deposition time. Electrodeposition occurred selectively into nanopores and the deposition on SiO2 layer was excluded. It was found out that Ni and Cu electrodeposited into nanopores of SiO2/Si system formed the same structures as at electrodeposition on the surface of monocrystalline n-Si-granules for Ni and scale-shaped particles for Cu deposits.