In order for assisted reproduction technologies to improve, better methods to discern eggs and embryos according to their level of developmental competence are urgently required to substitute or complement the subjective morphological selection criteria still broadly in use. Objective and reliable molecular markers of viability have been studied during the last decades as robust options to select the best oocytes and embryos for embryo transfer programs. These molecular methodologies rely mostly on the novel “OMICS” technologies. Among these, transcriptomicsis the primary platform applied so far in animal breeding research mainly due to the possibility to amplify small samples. In addition, biomarkers of competence have not only been instrumental to select the best oocytes and embryos for reproductive technologies, but have also shed light on the intricate molecular physiology leading to the acquisition of developmental capacity within the ovary and on how the embryo manifests this potential during culture. Nevertheless, such molecular profiling usually implies the destruction of the oocyte/embryo hereby preventing the practical use of biomarkers in in vitro embryo production and transfer systems. Alternatively, encouraging results have been lately obtained from non-invasive technologies based on biopsies of follicular somatic cells surrounding the developing egg, as well as from metabolic analysis of follicular fluid or spent culture media. This work summarizes the achievements of recent years in the field of biomarkers of competent bovine embryos. The main challenges will be exposed, while the future guidelines will help to comprehend why biomarkers of developmental competence appear promising to take us steps forward in the amelioration of reproductive technologies.