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Large proportions of hereditary breast cancers are due to mutations in the two breast cancer susceptibility genes BRCA1 and BRCA2. Considerable effort has gone into studying the function(s) of these tumor suppressor genes, both in attempts to better understand why individuals with these inherited mutations acquire breast (and ovarian) cancer and to potentially develop better treatment strategies. The advent of tools such as cDNA microarrays has enabled researchers to study global gene expression patterns in, for example, primary tumors, thus providing more comprehensive overviews of tumor development and progression. Our recent study (Hedenfalk et al., 2001) strongly supports the principle that genomic approaches to classification of hereditary breast cancers are possible, and that further studies will likely identify the most significant genes that discriminate between subgroups and may influence prognosis and treatment. A large number of hereditary breast cancer cases cannot be accounted for by mutations in these two genes and are believed to be due to as yet unidentified breast cancer predisposition genes (BRCAx). Subclassification of these non-BRCA1/2 breast cancers using cDNA microarray-based gene expression profiling, followed by linkage analysis and/or investigation of genomic alterations, may help in the recognition of novel breast cancer predisposition loci. To summarize, gene expression-based analysis of hereditary breast cancer can potentially be used for classification purposes, as well as to expand upon our knowledge of differences between different forms of hereditary breast cancer. Initial studies indicate that a patient's genotype does in fact leave an identifiable trace on her/his cancer's gene expression profile.