Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin to exit the neural fold/epidermal ectoderm boundary, we examined the facial mesenchyme, composed of neural crest and paraxial mesoderm cells, as well as cells from adjacent neuroepithelium. For these 11 samples, we used a single cell isolation and cDNA generation protocol followed by a standard Affymetrix labeling protocol to better define the gene expression states of the early E8.5 pioneer neural crest and paraxial mesoderm cells. Using a combination of statistical and expression level filtering criteria, we have identified expression patterns present within these embryonic cell populations. The genes identified through this study are highly enriched for known critical genes as well as many genes not previously known to be cell type specific at this stage. Overall design: Mouse emrbyos were harvested at developmental stage E8.5 and single cells were captured from the neuroepithilium, neural crest, and paraxial mesoderm. RNA was extracted, labelled, and quantified using the Mouse ST-l microarray. for further details about this study contact steve.potter@cchmc.org (isolation and labeling) or bruce.aronow@cchmc.org (informatics)