Breast cancer is a first magnitude problem of public health worldwide. There is increasing evidence that this cancer is originated in and maintained by a small population of undifferentiated cells with self-renewal properties. This small population generates a more differentiated pool of cells which represents the main mass of the tumor, resembling the hierarchical tissue organization of the normal breast. These cancer stem cells seem to share a similar phenotype with their normal counterparts but they display dysfunctional patterns of proliferation and differentiation, and they no longer respond to normal physiological controls that ensure a balanced cellular turnover. The origin of these cancer stem cells is controversial; it is not well known if they are originated from normal stem cells or from more differentiated progenitors where a de novo stem cell program is activated by the oncogenic insult. Here we review the origin of breast cancer stem cells and their role in the pathogenesis of cancer development, together with their implications in breast cancer progression, treatment and prognosis.