MAMMARY tumor stem cells have been described for several years. Identification of novel cell markers would be extremely useful in the identification of stem cells from normal and malignant tissue particularly those specific to stage. The skin stem cell marker CD29 (1- integrin) as well as CD49f (integrin 6) have been used to enrich a population of mouse MAMMARY cells from the stem cell population. Those cell surface markers are neither new nor restricted to the putative MAMMARY stem cell. Breast cancer stem cells have also been reported to highly express active aldehyde dehydrogenase (ALDH). Our goal was to identify novel markers on stem cells from pre cancer and malignant MAMMARY tissues. To accomplish this, we used combinatorial libraries to screen for novel peptides capable of binding to stem cells. Putative stem cells from pre cancer and tumor tissues from the breast were isolated by tissue dissociation and sorted by specific surface molecule expression or by ALDH expression. Lineage+ cells (CD45, CD31 and TER119) were excluded. Cells that expressed CD49f and various levels of CD24 and CD29 were used as putative stem cell populations as were cells expressing high levels of ALDH. Beads with bound cells were sequenced and the peptides used to search for putative stem cell binding sites and possible novel markers. Those sequences were motifs that would bind to the cancer stem cells. Analysis indicates acceptor molecules such as integrin /, cadherin, EGFR and procollagen on the surface of the stem cell. Structure-functional relationships are being assessed. Not only can the new markers be used to detect stem cells, but they can be used as a means for possibly differentiating between normal, pre cancer and tumor stem cells.