Breast cancer is a heterogeneous disease, composed of tumor cells with differing gene expressions and phenotypes. Tumor heterogeneity has several important consequences for breast cancer including: (i) making classification by morphological and expression analysis more difficult because of the diversity within single tumors with the consequence that the majority of cells of the tumor will dominate this classification whether or not these cells are critical for diagnosis or treatment, (ii) treatments may fail to eradicate tumors simply by failing to eliminate one of the cell subtypes within the tumor and (iii) differing abilities of the cell subtypes for dissemination and metastasis. Recently, a rare subpopulation of cells within tumors has been described with the ability to initiate and sustain tumor growth, to resist traditional therapies and to allow for secondary tumor dissemination. These cells are termed tumor-initiating cells (TICs) or cancer stem cells (CSCs), or alternatively, in the case of breast cancer breast cancer stem cells (BCSCs). The therapeutic targeting of these cells has the potential to eliminate residual disease and may become an important component of a multi-modality treatment. Here, we review the role of stem cells in the healthy breast, the role of breast cancer stem cells in disease, and the potential to target these cells.