During the past decade, several high throughput analytical methods for gene-expression profiling have been developed. DNA microarrays and multiplex RT-PCR have been applied in the field of breast-cancer research to establish new molecular taxonomic classifications, or a selected group of genes able to predict the prognosis of the patients and/or their response to chemotherapy. This technology provides an opportunity to refine the anti-neoplastic treatment and avoid the currently observed under- and over-treatment of breast-cancer patients. In parallel, high throughput technologies for gene-expression analysis have been applied to research on cancer stem cells (CSCs) and the tumor microenvironment, offering a wider vision of the molecular processes that influence carcinogenic events, disease development, and the response to the treatment of breast-cancer patients. In this report, we briefly revisit the most relevant genomic studies on breast-cancer prognosis and prediction to introduce the latest advances in tumor dormancy, its implications in the clinical outcome of disease-free patients and its connection with CSCs biology and microenvironment influence in the metastatic process. Finally, we have discussed the contribution of the results of these studies to the design of new experimental strategies oriented towards personalized medicine.