In order to understand the effects of all-trans-RA on palate development, RA was injected into the abdominal cavity of pregnant mice and then the embryos were taken in the following days and analyzed morphologically as well as molecular biologically. When RA was administered at the stage of E11 or E15, the overall craniofacial development was retarded. The length from jaw to eye was shortened, compared to that of normal group. When the E11 embryos were exposed to RA, cleft lip was also found along with the cleft palate. In vitro palate culture experiment also revealed that RA caused cleft palate. When RT-PCR was performed, early stage administration of RA at E11 inhibited the upregulation of Hoxa7 expression at E15 through E17. Whereas in control group, high level of Hoxa7 expression was detected in the palate of E15 to E17. In the case of Bax, the expression was decreased from E16, while remaining constant in control group. When TUNEL analysis was performed following the RA treatment at E15, TUNEL positive cells were detected in the mesenchymal cells as well as epithelial cells of palatal shelves of E16 and in E17 embryos. Whereas in normal control, TUNEL positive cells were observed mostly at the epithelium around the nasal cavity and oral cavity where rugae is made. These results altogether indicate that exposure to RA during palate development causes facial deformity including cleft palate and cleft lip by modulating the expression of homeotic genes such as Hoxa7 as well as an apoptosis-related gene, Bax, and thus malregulating the apoptosis.