We show that the detailed atomic structure of vacancy–impurity complexes in Si can be experimentally determined by combining positron lifetime and electron momentum distribution measurements. The vacancies complexed with a single impurity, V–P and V–As, are identified in electron irradiated Si. The formation of native vacancy defects is observed in highly As-doped Si at the doping level of 1020cm−3. The defects are identified as monovacancies surrounded by three As atoms. The formation of V–As3 complex is consistent with the theoretical descriptions of As diffusion and electrical deactivation in highly As doped Si.