Objective: To investigate the relationship between the content of cancer stem cells and clinicopathologic parameters of the patients with breast cancer, and the expressions and significances of P-glycoprotein (P-gp), glutathione S-transferase-π (GST-π), lung resistance protein (LRP) and topoisomerase II (TOPO-II) in breast cancer stem cells and differentiated breast cancer cells. Methods: Fresh tumor tissues from 30 invasive ductal carcinoma patients were mechanically dissociated into single cell suspensions, from which the cancer stem cells (CD44+/CD24– cells) and differentiated cancer cells (CD24+ and CD44–CD24– cells) were separated by two-step immunomagnetic sorting procedure and then counted. The relations of the content of cancer stem cells with the clinicopathologic variables of the patients were analyzed. The expressions of P-gp, GST-π, LRP and TOPO-II in the above two cells were determined by immunocytochemical staining. Results: The content of breast cancer stem cells was not clearly related to the age, tumor size, histological grade and lymph node metastasis of the patients (all P>0.05). Compared with differentiated cancer cells, the positive expression rate of P-gp was significantly elevated (73.3% vs. 40.0%) but TOPO-II was significantly decreased (40.0% vs. 76.7%) in breast cancer stem cells (P<0.05 or P<0.01). while the expressions of GST-π and LRP in the two types of cells showed no significant difference (both P>0.05). Conclusion: The content of cancer stem cells is not clearly associated with clinicopathologic parameters of breast cancer patients. However, breast cancer cells may contribute to chemotherapy resistance and recurrence of breast cancer due to their increased P-gp and decreased TOPO-II expression.