The bovine uterine microenvironment is a niche biological site in which the early embryo must complete several key developmental events before progressing on towards implantation and a successful pregnancy. From fertilization (Day 0) to hatching from the zona pellucida (~Day 10), embryo development is semi-autonomous. After hatching, the blastocyst stage embryo becomes completely dependent on endometrial secretions for survival and development, as evidenced in vivo by embryo death when the secretory uterine glands are ablated and by the inability to recapitulate embryo elongation in vitro. From hatching to implantation (~Day 30), the bovine embryo undergoes remarkable growth from an ovoid blastocyst 350 _m to a >20 cm filamentous embryo in the span of just ~25 days, driven by the rapid proliferation of mononuclear undifferentiated trophoblast cells. Amongst mammals, this extended period of preimplantation embryo elongation and delayed implantation until almost 1 month of pregnancy is unique and highlights the generative role of endometrial secretions for early ruminant embryo development. Notably, the timeframe for elongation is concurrent with high rates of early embryonic mortality (EEM) amongst high producing dairy cattle breeds such as the Holstein. Still, despite its biological interest to reproductive physiologists and economic importance to the dairy industry, little is known about the early life-sustaining uterine secretome, how the secretions change in profile and abundance across the estrous cycle, or their effects on embryos. My studies span the timeframe in which preimplantation embryo development takes place and address related questions about pregnancy. First, while my study on methods to enrich the low abundant bovine serum proteome was the most successful published to date, it demonstrates the need for antibody based depletion methods for future bovine serum pregnancy biomarker discovery. Second, my uterine research offers a new perspective on the uterine microenvironment by characterizing the cyclical endometrial secretions that compose uterine milk. By analyzing transcriptomics of endometrial biopsies through a secretory bioinformatics pipeline, I have profiled the stage-specific endometrial secretions that define the luminal fluid from sperm transit to embryo elongation. In parallel, I have complemented predicted endometrial protein secretions by characterizing the uterine fluid proteome at the same timepoints. Together, my endometrial transcriptomics and proteomics datasets are complementary to build a framework for understanding uterine derived factors influencing in utero embryo development. In addition to secretions, I have also considered the role of uterine luminal oxygen tension on embryonic development and measured the dissolved oxygen (pO2) in the uterine lumen across the estrous cycle and in bred heifers. From this, I learned that the uterine lumen is quasi-anoxic, and that the embryo develops in the presence of virtually no oxygen, a condition maintained by the uterine spiral artery vasculature. Finally, my research on reproductive physiology has extended to neonatal calf health by examining the postpartum kinetics of colostrum IgG secretion by the Holstein mammary gland demonstrates that 75% of all IgG is secreted after the first milking (within 2 hours postpartum), which in the context of the co-evolution of cow-calf physiology would suggest a second and third colostrum feeding at four and sixteen hours post-partum could impart immunological and developmental benefits to the neonatal calf. In sum, my systems biology research on bovine reproductive physiology improves our understanding of the temporal endometrial secretions that direct preimplantation embryo development in utero, and precisely defines the kinetics of postpartum IgG secretion and provides opportunities for sustained colostrum feeding for optimized neonatal calf health.