In mammalian species, the implanting embryo establishes physical and permanent interactions with the endometrium that require a tightly regulated and synchronized communication. In animal models, data have recently shown that perturbations of maternal physiology during the periconceptional period (e.g. nutrition) or manipulations of the preimplantation embryo conditions (e.g. in vitro culture, somatic cell nuclear transfer) are associated to developmental abnormalities that will impact pregnancy success with postnatal detrimental effects. Therefore analysing the sequences of events taking place during very early alterations of the endometrium–embryo dialogue may help in understanding long-term consequences. In ruminants, implantation occurs over a protracted period of time (10–15 days), allowing a step-by-step dissection of the molecular and cellular events. High-throughput tools (Evans et al., 2008) have been used to investigate early pregnancy, providing newinsights on the normal endometrial physiology during this period. Using pregnancies with distinct potentials of term development, we have generated endometrial gene profiles in cattle and demonstrated a differential response of the endometrium to IVF or SCNT embryos at implantation (Mansouri-Attia et al.,2009). The impact on several biological functions and various individual genes was profound when compared to control pregnancy, as independently confirmed in a companion paper (Bauersachs et al., 2009). From our data, we have proposed the endometrium as an early biological sensor of pregnancy that can fine-tune its physiology in response to embryo or maternal manipulations. Although placentation differs between cattle and human, we think that the sensing property of the endometrium is a common feature across mammals whose limits in plasticity deserve to be thoroughly investigated.