The polygenic and multifactor genetic basis of breast cancer confers to each tumour a different phenotype and clinical outcome. A therapeutic stake is to better determine this heterogeneity by using more reliable prognostic factors and to develop molecular therapies targeting the tumour cells selectively. The study of molecular alterations in breast cancer allowed considerable therapeutic progress by use of the hormonal receptors and the ERBB2 receptor. Today, new high-throughput technologies such as DNA microarrays allow measuring the activity of thousands of genes in a sample simultaneously. The awaited repercussions are multiple. Expression profiling of breast tumours allows the identification of new sub-groups of tumour in groups a priori identical, but with different outcome. This stratification should make it possible to better tailor the treatment and boost the discovery of new therapeutic targets