Bovine embryos are increasingly produced using reproductive technologies, e.g. ovum pick-up (OPU), in vitro embryo production (IVP) and embryo transfer (ET). Such in vitro manipulated embryos are known to deviate in several aspects compared to in vivo derived embryos. Pregnancy establishment in cattle involves timed biological events including fine-tuned communication, initiated and carried out by both the embryo and the endometrium. This stimulates research to increase the understanding of events and interactions taking place in the uterus after embryo transfer, both from a biological and systems biology point of view. This review will focus on the biological events taking place during early embryonic development, implantation and beginning of placentation, with focus on transfer of in vitro produced embryos, including a systems biology approach for selection of superior embryo recipients.