Mammary epithelial cells (MEC) undergo a series of developmental decisions during a pregnancy cycle. The switches from proliferation to differentiation to secretion and then to cell death are precisely controlled. In order to identify critical changes associated with the transition from a secretory phenotype during lactation to dedifferentiation and cell death, we have undertaken a microarray analysis of mouse mammary gland development. We have focused on the involution switch and on the transcription profiles of genes that are targets of transcription factors known to influence involution and apoptosis. Our results show that both Stat3 and NF-kB target genes are induced by the involution switch while Stat5 target genes are distinct from Stat3 induced genes. Furthermore, a substantial number of genes that were specifically upregulated at the start of involution are regulators of inflammation and the acute phase response. These results provide a novel insight into the involution process and demonstrate the value of microarray analysis in defining molecular events associated with critical developmental transitions in mammary gland.