We studied differential gene expression between normal breast epithelial cells and their malignant counterparts with a microarray technique, using GeneAlbum GEM (Incyte), which contains approximately 60,000 complementary DNA clones. We searched for different gene expression patterns among individuals, ages and races using four normal human mammary epithelial cells (HMEC). In addition, we used eight well-established breast cancer cell lines as probes against a common normal HMEC. Comparison between normal HMEC and malignant HMEC verified several known HMEC molecular markers: laminin-5 beta 3 and alpha 3, and cytokeratins 5, 15 and 17. We also observed some known breast-cancer-related genes, such as HER2, HER3 and pS2, which were expressed as expected. The microarray quantitation was verified independently using Taqman analysis. The results of flip-flop experiments are discussed, as are the distribution of differentially expressed genes in 11 probe pairs and their cluster analyses.