Gallium vacancies and negative ions are observed in GaN bulk crystals by applying positron lifetime spectroscopy. The concentration of Ga vacancies decreases with increasing Mg doping, as expected from the behavior of the VGa formation energy as a function of the Fermi level. The concentration of negative ions correlates with that of Mg impurities determined by secondary ion mass spectrometry. We thus attribute the negative ions to Mg−Ga. The negative charge of Mg suggests that Mg doping converts n-type GaN to semi-insulating mainly due to the electrical compensation of O+N donors by Mg−Ga acceptors.