Photoluminescence (PL) and Raman spectra of Ge/Si quantum dot (QD) structures grown using conventional molecular beam epitaxy, MBE, (sample M) and pulsed ion beam-assisted MBE (sample MI) were measured before and after vacuum annealing and hydrogen passivation. Two broad bands are observed in the PL spectra, one ascribed to the QDs and another one to radiation defects. Sample MI exhibits a higher overall PL intensity. The post-growth vacuum annealing partially suppresses the defect-related emission, enhances the QD-related PL in sample M, but almost does not affect the latter emission in sample MI. After the atomic hydrogen treatment that passivates the defect-related radiative and nonradiative recombination centers, a high-energy shift by 20-25 meV of the QD PL peak in sample MI appears when compared to sample M. The analysis shows that the shift is mainly due to a reduction of the QD size, which occurs in the case of the ion-assisted MBE. We conclude that the radiation defects created at the QD growth temperatures do not introduce nonradiative recombination channels, on the contrary to the defects caused by the nonequilibrium character of the MBE growth. In situ high-temperature ion bombardment during the QD growth pushes the epitaxial layer system towards equilibrium, thus enhancing the QD PL intensity. (c) 2008 Elsevier B.V. All rights reserved.