Epithelial-mesenchymal transformation (EMT) is the key mechanism for fusion and confluence of the rodent palate. During this process, medial edge epithelia (MEE) form a midline seam that subsequently transforms to mesenchymal cells. We studied syndecan-1 and E-cadherin, two molecules which have been shown to promote the epithelial phenotype, to determine their fate during palatal EMT. We found that both syndecan-1 and E-cadherin are expressed on basolateral surfaces of the MEE at day 14. Twelve hours later, when a midline seam has formed, syndecan-1 and E-cadherin are still present on its basal and lateral epithelial surfaces and they persist after the seam breaks up into epithelial islands. Then, expression of both molecules is lost simultaneously and abruptly when EMT occurs. On the contrary, previous in vitro studies of cell lines transfected with antisense cDNAs suggested that loss of syndecan-1 would lead to loss of E-cadherin or vice versa. We conclude that in vivo, synthesis of both E-cadherin and syndecan-1 is downregulated synchronously by the initiation of EMT, leading to an effective and correctly timed conversion of the epithelial cells to mesenchyme.