The mammary gland undergoes distinct periods of growth, development and secretory activity. During a bovine lactation, a gradual decrease in number of mammary epithelial cells largely accounts for the decline in milk production with advancing lactation. The net decline in cell number (~50%) is due to apoptotic cell death, but is accompanied by cell renewal. Though the rate of cell proliferation is slow, by end of lactation most cells in the gland were formed after calving. Typically milking is terminated when cows are in the final 2 mo of pregnancy. This causes regenerative involution, wherein there is extensive cell replacement and mammary growth. We hypothesized that replacement of senescent secretory cells and progenitor cells during the dry period increases milk yield in the next lactation. Analysis of global gene expression revealed networks and canonical pathways during regenerative involution that: support cell turnover and mammary growth, that are consistent with oxidative stress, mitochondrial dysfunction and ER-stress, as well as processes that ameliorate those effects, immune responses consistent with influx of neutrophils, macrophages and lymphocytes, and processes that support mammary differentiation and lactogenesis. Data also suggest that replication of stem/progenitor cells occurs during the dry period. Relying on long-term retention of bromodeoxyuridine-labeled DNA, we identified putative bovine mammary stem cells. These label retaining epithelial cells (LREC) are in low abundance within mammary epithelium (<1%), are predominantly estrogen receptor-negative and localized in a basal or suprabasal layer of the epithelium. Analyses of gene expression in laser-microdissected LREC are consistent with the concept that LREC represent stem cells and progenitor cells, which differ in properties and location within the epithelial layer. We identified potential markers for these cells and have increased their number by infusing xanthosine through the teat canal of prepubertal heifers. Altering population dynamics of mammary stem/progenitor cells during the mammary cycle may be a means to increase efficiency of milk production.