The lower layer of the pre-gastrulating chick embryo is an extra-embryonic tissue made up of two different cell populations, the hypoblast and the endoblast. The hypoblast is characterized by the expression of inhibitory signalling molecules (e.g. Cerberus, Dickkopf1, Crescent) and others (e.g. Otx2, goosecoid, Hex, Hesx1/RPX, FGF8). However, no genes expressed in the endoblast have yet been found. We designed a differential screen to identify markers differentially expressed in these two cell populations. This only revealed one novel gene, Apolipoprotein A1 (APO A1) with restricted endodermal layer expression. Expression of APO A1 begins very early throughout the lower layer (both hypoblast and endoblast). At later stages it is also expressed in the endoderm and its derivatives, the anterior intestinal portal endoderm and the growing liver bud.