The phenotypic diversity of breast cancer has been proposed to result from different target cell types undergoing oncogenic transformation and giving rise to cancer stem cells. Global gene expression profiling revealed distinct molecular phenotypes and some of these signatures were held to reflect the cell of origin, with the basal carcinomas arising from basal/progenitor cells. Recent work challenges this view by providing evidence that luminal precursor cells are involved in the pathogenesis of basal breast cancers and has made new links between normal cell populations and molecular tumor phenotypes.