The advent of microarray technology has enabled scientists to simultaneously investigate the expression of thousands of genes. Gene-expression profiling studies have provided a molecular classification of breast cancer into clinically relevant subtypes, new tools to predict disease recurrence and response to different treatments, and new insights into various oncogenic pathways and the process of metastatic progression. Here we describe the state of the art of gene-expression studies in breast cancer, and consider both their current limitations and future promises. We also discuss the potential of molecular signatures to have an impact on individual breast cancer patient management, and ultimately to accelerate the transition between empirical and tailored medicine.