Recent evidence suggests that most malignancies are driven by "cancer stem cells" sharing the signature characteristics of adult stem cells: the ability to self renew and to differentiate. Furthermore these cells are thought to be quiescent, infrequently dividing cells with a natural resistance to chemotherapeutic agents. These studies theorize that therapies, which effectively treat the majority of tumor cells but 'miss' the stem cell population, will fail, while therapies directed at stern cells can potentially eradicate tumors. In breast cancer, researchers have isolated 'breast cancer stein cells' capable of recreating the tumor in vivo and in vitro. Generated new tumors contained both additional numbers of cancer stem cells and diverse mixed populations of cells present in the initial tumor, supporting the intriguing self-renewal and differentiation characteristics. In the present study, an antibody phage library has been used to search for phage displayed-single chain antibodies (scFv) with selective affinity to specific targets on breast cancer stem cells. We demonstrate evidence of two clones binding specifically to a cancer stem cell population isolated from the SUM159 breast cancer cell line. These clones had selective affinity for cancer stein cells and they were able to select cancer stem cells among a large population of non-stem cancer cells in paraffin-em bedded sections. The applicability of these clones to paraffin sections and frozen tissue specimens made them good candidates to be used as diagnostic and prognostic markers in breast cancer patient samples taking into consideration the cancer stern cell concept in tumor biology. (C) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 25: 1780-1787, 2009