Vacancy-type defects in plasma immersion B-implanted Si were probed by a monoenergetic positron beam. A positron annihilates with an electron and emits two 511 keV γ-quanta. Doppler broadening spectra of the annihilation radiation were measured and compared with spectra calculated using the first-principles calculations. For the as-doped sample, the vacancy-rich region was found to be localized within 0-10 nm from the surface, and the major defect species were determined to be divacancy-B complexes. After spike rapid thermal annealing at 1075°C, those complexes were annealed out, and turned to B clusters such as icosahedral B12 distributed between 4 nm and 32 nm from the surface. We will demonstrate that that the positron annihilation technique is sensitive to point defects in shallow junctions formed on Si substrates without influence of B atoms located in the substitutional site.