In cattle, the developing preimplantation conceptus depends solely on its surrounding environment for supplying nutrients and growth stimuli. Also, throughout gestation, it is during the preimplantation stage of gestation that most conceptus mortality is observed. Thus, one could rationalize that the composition of the uterine environment plays a major role on conceptus survival. However, the biochemical composition of the uterine environment is only just starting to be deciphered and conditions associated with optimal conceptus development are virtually unknown. In this review we attempt to briefly review and discuss issues associated with sampling and analyzing the uterine environment. We suggest that modern, holistic approaches such as Systems Biology are necessary to characterize the uterine functions associated with pregnancy success in cattle.