The Goosecoid (gsc) gene is a homeobox-containing gene expressed first in the gastrula, and later during organogenesis in development. The gsc gene transcript is found in the first and second branchial arches, frontonasal mass in its late phase of expression. We have previously shown that targeted mutation of the mouse gsc gene leads to neonatal death and craniofacial defects. In this study, we performed histological studies on craniofacial phenotypes in order to elucidate the processes underlying the neonatal death of gsc mutant mice. We found that gsc mutant mice have aplastic nasal cavities and lack the Sinus Paranasalis. We also showed that secretory olfactory glands in the basal layers are aplastic. This is suggested to be essential defects for olfaction. gsc mutant mice also show several pharyngeal phenotypes, including defects in the pharyngeal muscles and the pharyngeal mucosa. It is therefore suggested that mutant mice develop lethal gastro-intestinal phenotypes caused by defects in breathing and sucking of milk as a consequence of these craniofacial disorders. These results should help elucidating the molecular genetic programs essential to the neonatal development of mammals.