The recent advent of high-density cDNA microarray technology, with its capacity for simultaneous monitoring of thousands of genes, provides a unique opportunity for high-throughput genetic analysis of cancer. Although most current microarray studies have been performed with in vitro-derived genetic material, a major leap in functional genomic investigations would be the ability to perform array-based expression analysis with in vivo-derived genetic material originating from morphologically distinct cellular populations, including various stages of cancer progression. Until recently, in vivo analysis of tumour-specific genomic alterations, array-based or otherwise, has been hampered by the inability to accurately obtain specific cell types from cancerous tissue. The recent development of laser capture microdissection (LCM) has allowed for accurate and rapid procurement of specific cell populations in complex tissue and provides the opportunity to perform array-based expression profiling of in vivo-derived genetic material. Here we describe the combined use of LCM, high-throughput cDNA microarrays and Taqman real-time quantitative PCR (RTQ-PCR) to monitor gene expression levels in breast cancer. We demonstrate that expression profiles of greater than 8,000 genes can be successfully generated using non-amplified RNA derived from distinct cell populations in several different morphological stages of human breast cancer.