MicroRNAs (miRNAs), non-coding RNAs that function as post-transcriptional gene regulators, play a pivotal role in cancer development. In the present study, we elucidated the roles of miR-520b and miR-520e in breast cancer cells. We examined the expression levels of miR-520b and miR-520e in the immortalized breast cell line, HBL-100, and in three breast cancer cell lines: MCF-7, LM-MCF-7 and MDA-MB-231. We show the expression levels of miR-520b and miR-520e in the breast cancer cell lines were lower than that in the HBL-100 cells. Furthermore, the breast cancer cell lines showed less sensitivity to complement-dependent cytotoxicity (CDC). We found that overexpression of miR-520b and miR-520e increases the sensitivity of the breast cancer cells to CDC, whereas further suppression of miR-520b and miR-520e decreases the sensitivity of the breast cancer cells to CDC. We then demonstrate that miR-520b and miR-520e are able to directly target the 3'untranslated regions (3'UTR) of the membrane-bound complement regulatory protein CD46; suggesting that miR-520b and miR-520e down-regulate CD46 at post-transcriptional level. Enzyme-linked immunosorbent assay (ELISA) showed that overexpression of miR-520b and miR-520e results in the increased expression of C3b, which is mediated by downregulated CD46. These results suggest that miRNA-520b and miR-520e mediated down-regulation of CD46 induces opsonization of cancer cells via an alternative pathway resulting in complement activation. Thus, we conclude that miR-520b and miR-520e contribute to CDC in breast cancer cells via directly targeting the 3'UTR of CD46.