Regular removal of milk from the mammary gland is critical to maintaining milk secretion. Early studies in rodents demonstrated that changes in milking frequency influenced mammary blood flow, as well as mammary cell number and activity. Later studies in ruminants confirmed those observations and that the response was regulated locally within the mammary gland. In addition, it was discovered that increased milking frequency (IMF) during early lactation stimulated an increase in milk production that partially persisted through late lactation, indicating long-term effects on mammary function. The local mechanisms regulating the mammary response to IMF are poorly understood, although several have been proposed. To gain insight into the mechanisms underlying the mammary response to IMF, and to identify genes associated with the response, we used a functional genomics approach and conducted experiments on dairy cows exposed to unilateral frequent milking [UFM; twice daily milking (2X) of the left udder half and 4-times daily milking (4X) of the right udder half]. Across multiple experiments, we were unable to detect an effect of UFM on mammary cell proliferation or apoptosis. We have, however, identified distinct transcriptional signatures associated with the mammary response to milk removal and to UFM during early lactation. Sequential sampling of mammary tissue revealed that when UFM was imposed during early lactation, at least 2 sets of genes were coordinately regulated with changes in differential milk production of 4X vs. 2X udder halves. Moreover, some genes were persistently differentially expressed in 4X vs. 2X udder halves after UFM and were associated with the persistent increase in milk yield. We conclude that a coordinated transcriptional response is associated with the increase in milk yield elicited by IMF during early lactation and that the 2 sets of differentially expressed genes may be a marker for the autocrine up-regulation of milk production. Moreover, we propose that we have identified a novel form of imprinting associated with persistent alteration of mammary function, which we term "lactational imprinting."