Objectives: Aim of the study was to reveal new biomarker genes to target breast cancer stem-like cells (BCSC-like) and then sensitize BCSC-like cells to chemotherapy by silencing MDR1 gene found to be the most suitable target. Methods: Drug resistance associated genes were screened by cDNA microarray to unveil biomarker genes in drug resistance breast cancer model cells. Drug resistance was then reversed by silencing MDR1 gene in BCSC-like cells. The effect of silencing was monitored by real-time cell proliferation analysis. Differential expressions of MDR1, ALDH1A3, EGFR and BAG4 genes were identified by real-time PCR. P-glycoprotein (P-gp) expression level and its activity were investigated by Western blot and flow cytometry measurements, respectively. Results: 16 new biomarker genes were identified upon gene expression analysis by cDNA microarray. MDR1 gene was selected as the most potent target gene and silencing of it caused down-regulation of MDR1, ALDH1A3, EGFR, BAG4 expression and P-glycoprotein activity and expression in BCSC-like cells. At the end, silenced BCSC-like cells were found to be more responsive to paclitaxel therapy. Conclusions: In conclusion, siMDR1 silencing is an effective way to reverse multidrug resistance and malignancy. New biomarker genes revealed in this study require to be investigated to target stemness of BC.