In the mouse blastocyst, Eomes and Cdx2 are critical for establishing the trophoectoderm, the precursor of the placenta. To better understand how the trophoectoderm lineage arose in mammals during evolution, we examined the expression of their orthologues in the pregastrulation chick embryo and found that, while both genes are expressed in extraembryonic tissues, their temporal pattern of expression differs from what occurs in mouse. Moreover, we failed to detect expression of other genes specific from the mouse trophoectoderm in extraembryonic regions of the chick. Also unlike the mouse, chick Eomes is expressed in primordial germ cells. Finally, conserved noncoding elements in the Eomes genomic region are unable to drive trophoectoderm restricted expression in the mouse blastocyst, but do so in conserved sites of expression such as the forebrain. These results suggest that critical changes in the gene regulatory networks controlling extraembryonic development accompanied the appearance of the trophoectoderm in mammals. Developmental Dynamics 239:620–629, 2010. © 2009 Wiley-Liss, Inc.