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Molecular-beam epitaxy (MBE) has been utilized to grow Si-doped GaN layers on GaN/sapphire templates prepared by hydride vapor phase epitaxy. An extensive set of characterization techniques is applied to investigate the layers. Positron annihilation experiments indicate that the samples contain open volume defects, most likely clusters of vacancies and possibly Ga vacancy-donor complexes. The number of vacancy clusters decreases, as Si concentration is increased. Photoluminescence spectra show that while the absolute intensity of both the yellow and ultraviolet (UV) band-edge transitions increase with Si doping, the intensity ratio of yellow-to-UV emission is decreased. Secondary ion mass spectrometry indicates that the impurity concentrations are in qualitative agreement with the carrier concentrations determined in electrical experiments. The data suggest further that silicon does not affect the diffusion of oxygen. Moreover, transmission electron microscopy reveals that MBE-grown GaN retains the threading dislocation structure of the GaN/sapphire substrate. The MBE layer is also shown to grow in the Ga face orientation, but some inversion boundaries are present in the epilayer. © 2002 American Institute of Physics.