During palatogenesis, the palatal medial edge epithelium (MEE) forms the medial epithelial seam (MES) on adhesion of the opposing palatal shelves. The MES eventually disappears, leading to mesenchymal confluence of the palate and completion of palatogenesis. Failure of these processes results in cleft palate, one of the most common congenital anomalies in human affecting around one case in 500–2500 live births. The cell fate of MEE has been controversial for more than 20 years. Recent studies suggest that the disappearance of MES is a complex process involving cell death, epithelial‐mesenchymal transition (EMT) and epithelial migration. Interestingly, transforming growth factor‐β3 (Tgf β3) expression in MEE and the tip epithelium of the nasal septum begins just before palatal shelf reorientation and lasts until MES disruption, and several works including targeted disruption of the gene have indicated that the process appears to be regulated mainly by the TGFβ3‐TGFβR signaling. However, how MEE cells choose their fate and how the cell fate is altered in response to cellular environment remains to be elucidated.