Emerging evidence from a variety of tissue types, including the mammary gland, suggests that normal stem and progenitor cells are the likely targets for malignant transformation, and that these transformed cells can function as cancer stem cells that drive tumour growth. In order to develop therapies that target these cancer stem cells, it is essential to determine the molecular mechanisms that regulate the growth and differentiation of these cells and their normal counterparts. To this end, a number of quantitative robust clonal assays have been developed that can detect the presence of human and mouse mammary stem and progenitor cells. These assays, when used in conjunction with cell-sorting strategies, have permitted the prospective isolation and characterization of a variety of cell types, including stem cells. Evidence to date indicates that these stem cells exhibit properties of basal mammary cells, possess extensive self-renewal properties, and are capable of generating a large number of phenotypically-distinct progenitor cells, many of which display characteristics of luminal cells. This review article will focus on the assays used to detect mammary stem and progenitor cells, some of the properties of these cells and their progeny and how they relate to the cancer stem cells that drive breast tumour growth. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.