The cancer stem cell theory poses that cancers develop from a subset of malignant cells that possess stem cell characteristics and has been proposed to account for the development of a variety of malignancies, including breast cancer. These cancer stem cells (CSC) possess characteristics of both stem cells and cancer cells, in that they have the properties of self-renewal, asymmetric cell division, resistance to apoptosis, independent growth, tumourigenicity and metastatic potential. A CSC origin for breast cancer can neatly explain both the heterogeneity of breast cancers and the relapse of the tumours after treatment. However, many reports on CSC in the breast are contradictory. There is variation with respect to how breast cancer stem cells should be identified, their characteristics and a possible lack of correlation between clinical outcome and breast cancer stem cell status of a tumour. These combined factors have made breast cancer stem cells a highly contentious issue. In this review, we highlight the progress in the analysis of cancer stem cells, with an emphasis on breast cancer.