Overexpression of breast cancer resistance protein (ABCG2/BCRP) in cancer cells may cause tumor resistance to chemotherapeutic drugs. RNA interference (RNAi) can selectively silence the expression of a target gene of interest. In the present study, we aimed to modulate the BCRP expression and examine the functional consequence using RNAi approach. Three siRNAs (si-BCRP1, si-BCRP2 and si-BCRP3) targeting BCRP were evaluated in drug-resistant MCF-7/MX100 cells overexpressing BCRP. The BCRP expression at the mRNA and protein levels was inhibited by si-BCRP2 and si-BCRP3 over 90% and 70%, respectively. As a result, the intracellular mitoxantrone accumulation was sharply increased in MCF-7/ MX100 cells after the transfection. Furthermore, shRNA sequences bearing si-BCRP2 and siBCRP3 were cloned into lentiviral expression plasmid (pTRIPZ) to package lentivirus, and MCF-7/MX100 cells stably expressing siRNA targeted to human ABCG2/BCRP were established by lentivector-mediated gene transfer system. The stable cells exhibited an increased miotxantrone accumulation, among which the BCRP expression at the mRNA level was reduced by Lenti-BCRP2 and Lenti-BCRP3 around 72% and 56%, respectively. Moreover, the BCRP expression at the protein level was reduced by 70% and 53%, respectively. Furthermore, the cell lines were used to screen active ingredients in traditional herbal medicines in order to evaluate BCRP substrates or inhibitors. Our data suggested that the BCRP knockdown cell lines could serve as good cell models for preclinical studies.