Array technologies create an opportunity to identify diagnostic and prognostic markers, as well as drug targets, from clinical samples. We have developed a mid-density spotted oligonucleotide array platform for monitoring gene expression and genomic amplification and loss events in human tumours. The spotted oligo arrays are sensitive, robust and allow rapid incorporation of new sequence information. We have also designed a single custom Affymetrix GeneChip™ array to monitor 35,000 genes and ESTs by empirically choosing probes on the basis of consistent performance over a wide range of samples. Integration of gene expression data from Affymetrix and Eos oligo arrays, in conjunction with genome amplification data, has identified a number of transcripts with increased mRNA expression and genomic representation in breast cancer. We have further generated a normal tissue atlas database that allows us to screen potential drug leads for possible toxic side effects. Candidate disease genes identified by DNA microarrays are then used to interrogate arrayed archival tumour tissues in a highly parallel fashion by in situ hybridisation. These tumour tissue microarrays allow for the rapid characterisation of expression at single cell resolution. In addition, gene expression can be associated with tumour grade and stage on hundreds of archival tumours with known clinical outcomes. Using these multiple array technologies we have identified a number of transcripts expected to encode tumour-specific proteins which are potential targets for therapeutic intervention, diagnosis and prognosis of breast cancer.