During development of the mouse conceptus from implantation to the early gastrula stage, a multitude of genes encoding structural proteins, transcription factors and components of signalling pathways are expressed in the extraembryonic and embryonic tissues derived from the trophectoderm and the inner cell mass. Some genes are expressed widely in the extraembryonic ectoderm, the visceral endoderm or the epiblast, while others display more restricted expression domains in these tissues or are expressed upon the specification of the germ layers at gastrulation. Overall, the developmental changes in gene expression mirror key events of embryogenesis, and reveal the regionalization of signalling activity and the emergence of tissue patterning.