Deep centers in Si-doped n-GaN layers grown by reactive molecular beam epitaxy have been studied by deep-level transient spectroscopy as a function of growth conditions. Si-doped GaN samples grown on a Si-doped n+-GaN contact layer at 800 °C show a dominant trap C1 with activation energy ET = 0.44 eV and capture cross-section σT = 1.3×10−15 cm−2, while samples grown at 750 °C on an undoped semi-insulating GaN buffer show prominent traps D1 and E1, with ET = 0.20 eV and σT = 8.4×10−17 cm2, and ET = 0.21 eV and σT = 1.6×10−14 cm2, respectively. Trap E1 is believed to be related to a N-vacancy defect, since the Arrhenius signature for E1 is very similar to the previously reported trap E, which is produced by 1-MeV electron irradiation in GaN materials grown by both metalorganic chemical-vapor deposition and hydride vapor-phase epitaxy.