Clefts of the secondary palate are among the most frequent birth defects in live-born human infants. Across the United States between 1981 and 1995, a compilation of data from states with birth defects monitoring programs shows the incidence of cleft palate without cleft lip to range from 2.01 to 14.2 per 10,000 live births (1 ). Thus, the formation of the secondary palate and the mechanism(s) for induction of cleft palate have been the focus of extensive research. Palatogenesis also presents an interesting model for many of the processes involved in morphogenesis in the embryo. The formation of the secondary palate requires neural crest cell migration, interaction of the palatal cells with the surrounding extracellular matrix, interaction and signaling between epithelial and mesenchymal cells, adhesion and fusion of morphological structures, which also involves cell death and transformation of cells from epithelial to mesenchymal phenotypes, and, finally, differentiation into bone and stratified oral and ciliated nasal epithelia (2 ). In order to study these processes and the potential of exogenous agents to disrupt them, in vitro models have been developed, including mesenchymal cell culture, epithelial cell culture, and palatal organ culture. Palatal organ culture can be a system in which the palatal shelves are supported on a membrane above the medium; our laboratory has used this method in the past (3 -5 ). However, the model described in this chapter is a submerged culture of the entire midfacial region. This model offers several advantages over the earlier system, as it permits the palatal shelves to grow, elevate, and fuse in the culture medium. This model has been tested in our laboratory for several strains of rat and mouse, and it has supported development of the palate in human embryonic midfacial tissue (6 ). Examples of the application of this culture model include studies of the effects of methanol and 5-fluorouracil on palatogenesis (7 -9 ).