To gain insight into the regulation mechanism associated with retinoic acid (RA) induced cleft palate, gene expression profiles of secondary palate on embryonic day 14 was investigated by using Affymetrix Mouse Gene Chip. RA-induced cleft palate mouse model was made, 27 cleft palate embryos and 18 embryos in control group on embryonic day 14 were harvested. Related genes were examined in the palate of these mice by genechip. Using the twice significance of difference as the standard, totally there were 81 up-regulated transcripts and 1249 down-regulated ones in RA-treated group compared with control group, gene functional categories and pathways, particularly involved in transcription regulator activity, regulation of growth, direction of cell movement, cytoskeleton, Wnt and Hedgehog families as well as actin cytoskeleton pathway were identified. These data proved that growth inhibition is the main cause for cleft palate formation treated by RA in the stage, meanwhile, cell movement, intracellular transport and cell division are also involved through interaction of Wnt and Hedgehog pathway with RA singnaling. It has highlighted potential cascades and important candidates for further investigation on the genetic mechanism and clinical therapy of cleft palate.