The advent of microarray tools has generated a massive amount of gene expression data. These data have greatly enhanced our understanding of the biology of breast cancer metastasis and provide a way to improve the prediction of the metastatic potential of breast tumours. Gene-expression profiling has highlighted the molecular heterogeneity of mammary tumours and contributed to the identification of a new molecular classification of breast cancers. In addition, several molecular signatures predicting the likelihood of distant metastases for breast cancer patients have been characterized. Further reports have described gene expression profiles associated with specific metastatic phenotypes, including the organ preference of breast cancer metastasis. Here we review the major studies that had important impacts on the understanding of breast cancer metastasis. We also discuss the future challenges in this research field and the special issues that still need to be examined.