BRCA1 is an important tumor suppressor gene associated with inherited breast and ovarian cancers. In this investigation, two novel BRCA1 splicing variants were cloned from breast cancer cell line ZR-75-30. These transcripts, named BRCA1-PI21-Delta2-21 and BRCA1-Delta2-14, lacked most exons of full length BRCA1 gene, but maintained the original reading frame. We also demonstrated the presence of BRCA1-PI21-Delta2-21 in several human cell lines. Expression of both variants fused with green fluorescent protein (GFP) showed that they targeted different subcellular compartments in the transfected cells. Viability of the cells expressing both fusion proteins decreased notably compared with the viability of cells expressing only GFP. Fluorescence activated cell sorting assay confirmed that the overexpression of two splicing variants resulted in cell apoptosis. Taken together, the different subcellular localization and cell effects of two BRCA1 splicing variants imply that they can have different biological functions in breast cancer cells. Elucidating the functions of BRCA1 splicing variants would help to understand the exact roles of the BRCA1 gene in tumor suppression.