Completion of the human genome project has revolutionised translational medicine. High-throughput technology now permits investigators to systematically interrogate the genome, transcriptome, proteome and metabolome. It is expected that these advances will eventually be translated into new more sensitive diagnostic tests and less toxic therapeutics. A major shift is expected in clinical oncology over the next few decades as we start to move away from currently practiced, population-based approaches to personalised medicine. In this emerging approach, the molecular and pathophysiological characteristics of an individual patient and tumour will be measured and tailored therapeutic regimens will be administered based on these profiles. One of the key steps in this process will be the identification and validation of biomarkers. Whilst great advances have been made in the discovery of putative biomarkers, disappointingly few have been translated into clinically applicable assays. It is widely believed that this is due to a lack of well-designed, thorough validation studies. Here, we review the role of DNA microarrays and tissue microarrays in the validation of biomarkers in breast cancer, with emphasis on their potential application to determine mode of personalised therapy in the future.