This review takes a sceptical view of the impact of breast cancer studies that have used microarrays to identify predictors of clinical outcome. In addition to discussing general pitfalls of microarray experiments, we also critically review the key breast cancer studies to highlight methodological problems in cohort selection, statistical analysis, validation of results and reporting of raw data. We conclude that the optimum use of microarrays in clinical studies requires further optimisation and standardisation of methodology and reporting, together with improvements in clinical study design.