We have applied positron annihilation to study point defects in 2 MeV 4He+-irradiated and subsequently rapid-thermal-annealed (RTA) InN grown by molecular-beam epitaxy. The irradiation fluences ranged from 5×1014 to 2×1016 cm−2. The irradiation primarily produces donor defects but the subjects of this work are the acceptor-type defects produced in lower concentrations: VIn, in addition to negative-ion-type defects. The heat treatment results in a redistribution of the irradiation-induced point defects. The In vacancies near the film-substrate interface appear restructured after the RTA process, possibly influenced by growth defects near the interface, while deeper in the InN layer, the defects produced in the irradiation are partially removed in the annealing. This could be responsible for the improved transport properties of the annealed films.