The core of the hierarchical adult mammalian haematopoietic system is formed by haematopoietic stem cells (HSC), which are multipotent cells with self-renewing properties. Embryonic development of the hematopoietic system is highly dynamic with different organs participating. The origin of definitive HSC in the mid-gestation mouse conceptus is attributed to a rare subset of endothelial cells, termed haemogenic endothelial cells. The occurrence of haemogenic endothelial cells is spatially restricted to the vitelline and umbilical vessels, the dorsal aorta, the extra-embryonic yolk sac and placenta as well as vessels in the embryonic head. The embryonic hematopoietic niches are poorly characterized. This study analyses gene expression across haemogenic and non-haemogenic tissues derived from mouse conceptus aged between 9.5 and 13.5 days post coitum (d.p.c.). Transcriptome studies showed that a small subset of genes was up regulated at the 12.5 d.p.c. yolk sac, when haemogenic activity is lost. Surprisingly, most of these highly up-regulated genes are members of the prolactin receptor, cathepsin and carcinoembryonic antigen (CEA) gene families. Members of these families encode hormones, enzymes and adhesion molecules, respectively. Our recent findings demonstrate that some of these genes, previously described as “placenta-specific” are indeed expressed in the yolk sac. Further studies will determine if yolk sac up regulated genes are linked to haematopoietic activity and endothelial cell function.