Despite their biological and biotechnological interest, pluripotent embryonic stem cell lines (ES cells) have been isolated from cultured embryos only in a very limited number of mammalian species. Here we review the main molecular mechanisms that have been shown in mouse or primates to regulate the maintenance of pluripotency in vitro. We describe the main signaling pathways that participate in the self-renewal of ES cells and provide an outlook on the epigenetic associated mechanisms. We also propose a practical approach to stem cell differentiation that examines the relationships between the genotype of embryos and their culture conditions and consider nuclear reprogramming as a valuable approach in ES cell derivation in farm animals.