The Foxd3 forkhead transcription factor is required for maintaining pluripotent cells in the early mouse embryo and for the establishment of murine embryonic stem cell (ESC) lines. To begin to understand the role of Foxd3 in ESC maintenance, we derived ESC lines from blastocysts that carried two conditional Foxd3 alleles and a tamoxifen-inducible Cre transgene. Tamoxifen treatment produced a rapid and near complete loss of Foxd3 mRNA and protein. Foxd3-deficient ESCs maintained a normal proliferation rate but displayed increased apoptosis, and clonally dispersed ESCs showed a decreased ability to self-renew. Under either self-renewal or differentiation-promoting culture conditions we observed a strong, precocious differentiation of Foxd3 mutant ESCs along multiple lineages, including trophectoderm, endoderm, and mesendoderm. This profound alteration in biological behavior occurred in the face of continued expression of factors known to induce pluripotency, including Oct4, Sox2, and Nanog. We present a model for the role of Foxd3 in repressing differentiation, promoting self-renewal, and maintaining survival of mouse ESCs. Disclosure of potential conflicts of interest is found at the end of this article.