Conceptus-maternal communication is vital for the successful establishment and maintenance of pregnancy, yet relatively little information exists for many of the mechanisms and the nature of the conceptus signals responsible for this cross-talk. Sub-optimal communication, resulting from impairment of conceptus development and/or from abnormal uterine receptivity, contributes to a high incidence of embryonic mortality. Therefore, detailed examination of the mechanisms regulating both pre- and peri-implantation conceptus development are necessary to fully understand the factors regulating successful post-hatching development, pregnancy recognition and implantation signaling. Despite significant progress in understanding of the temporal changes in the transcriptome of the uterine endometrium, there is only a rudimentary knowledge of the genes and pathways governing growth and development of the cattle conceptus. Furthermore, although there are a large number of studies describing gene expression profiles in bovine embryos focused mainly during the earlier preimplantation stages (up to and including Day 7), very little information exists for the post-hatching embryo and elongating conceptus. This period of development is arguably more important as a significant proportion of all embryonic loss occurs between Days 8 and 16 of pregnancy in cattle, corresponding to the time of hatching of the blastocyst from the zona pellucida and its subsequent elongation coincident with the time of maternal recognition of pregnancy. Given that this is a critical period in development leading up to maternal recognition and establishment of pregnancy, the identification of key genes and pathways regulating these crucial developmental events is essential.