Genomic rearrangement occasionally affects the BRCA1/2 genes in Caucasian breast cancer patients. However, the incidence of BRCA1/2 genomic rearrangement in Asians, including the Korean population, has not been well established. Here, we investigated the contribution of BRCA1/2 genomic rearrangement to high-risk breast cancer patients in this population. We screened for BRCA1/2 genomic rearrangement using multiplex ligation-dependent probe amplification for 122 high-risk breast cancer patients who tested negative for BRCA1/2 mutations. A novel deletion of exons 13-15 in BRCA1 was identified in one patient (0.8% occurrence frequency). Further analyses revealed that this c.4186-1593_4676-1465del might be the result of homologous recombination mediated by two Alu-elements: the AluY in intron 12, and an AluSp in intron 15. This result suggests that subsequent screening for BRCA1/2 genomic rearrangements should be considered in high-risk Korean breast cancer patients who test negative for BRCA1/2 mutations. BRCA1/2 genomic rearrangement, however, is likely to make only a small contribution to breast cancer in this population.