65-80% of the patients with breast cancer might not benefit from the adjuvant therapy they receive based on 'classical' markers used for the selection for adjuvant therapy. Therefore it is necessary to develop new markers that are able to tailor treatment for an individual patient. A number of microarray methods have been developed in recent years to accommodate this search for new factors that determine breast cancer progression. We give an overview of the most commonly used microarray methods to identify tumour progression markers (oligo- or cDNA arrays, CGH arrays, PCR arrays, and tissue microarrays). Their applications will be illustrated using the most influential examples from literature. The potentials, limitations and the related statistical analyses of each method are discussed. We conclude that microarray studies have led to an increase in the understanding of the complexity and diversity of breast carcinoma and have provided clinical relevant subgroups of breast cancer that may benefit from patient tailored treatment. Still, more extensive external validation and long-term follow-up will be necessary before such assays can be implemented into routine clinical practice. Most likely, these novel prognostic indicators will be complementary to the already available classical prognostic factors. (C) 2008 Elsevier Ireland Ltd. All rights reserved.