Tumour-initiating cells (TICs) have been suggested to arise through the activation of normal stem cell programmes, including those driving epithelial-to-mesenchymal transition (EMT). Ye et al. report that although both mammary stem cells (MaSCs) and TICs undergo EMT, the underlying programmes induced in these cells are different. Previous studies have relied on xenograft models and ectopic expression of EMT transcription factors, such as the paralogues SNAIL and SLUG. In this study, the authors used genetically engineered mice expressing reporter constructs that mimic endogenous SNAIL or SLUG expression to show that while SLUG was highly expressed in MaSCs, SNAIL was induced in mammary tumour cells exhibiting mesenchymal traits. Several lines of evidence suggested that SNAIL expression was associated with a tumour-initiating phenotype, whereas SLUG expression was not. Furthermore, the transcription programmes controlled by SNAIL and SLUG in mammary tumour cells differed. This suggests that MaSCs and TICs might also use different signalling circuits to induce EMT.