The epithelial compartment of the human breast comprises two distinct cell types. Type I human breast epithelial cells (HBECs) are expressing luminal epithelial cell markers and stem cell characteristics, whereas Type II HBECs show basal epithelial cell phenotypes. When defined in terms of markers for normal cell lineages, most invasive breast cancer cells correspond to the phenotype of the common luminal epithelial cell. We had developed simian virus 40-immortalized cell lines from normal HBECs with luminal and stem cell characteristics. To identify molecular changes involved in immortalization, we analyzed the differential gene expression profiles of normal and non-tumorigenic immortalized Type I HBECs using cDNA microarray with 7,448 sequence-verified clones. Out of the 7,448 genes screened, consistent gene expression changes among biological replicates included 67 in Type I HBECs and 86 in Type II HBECs for 4-fold change criteria. Surprisingly, we identified 148 genes (>2.0-fold) as being either up- or down-regulated related to immortalization: 67 genes (MYBL2, UCHL1 et al) were up-regulated, and 81 genes (IGFBP3, CDKN1A et al) were down-regulated significantly. The altered expression levels of the selected genes were subsequently confirmed by semiquantitative RT-PCR. Our studies suggest that the immortalization of Type I HBECs might be an early step in the initiation of a subset of breast cancer. Furthermore, these results will open up an avenue for more detailed understanding of breast stem cell and tumor biology.