Cleft palate is a common craniofacial birth defect. The aim of the present study was to investigate the effect of excess all-trans retinoic acid (atRA) on periderm removal and the disappearance of basal medial edge epithelial (MEE) cells during palatogenesis, particularly during the stage prior to contact. atRA (200 mg/kg) was administered to C57BL/6N mice at embryonic day (E) 12.0 by gavage. Fetal palates were processed and analyzed by histology and electron microscopy. Single palate shelf peridermal cells were removed and cultured in the presence of atRA (3 µM) only or in the presence of or the caspase inhibitor, Z-VAD (100 µM) only, for 48 h. Once cultured, morphological changes were analyzed by histological staining and electron microscopy. A TUNEL assay was used to detect apoptotic neurons. Paired palatal shelves with periderm removal were cultured in the presence of atRA (3 µM) only or in the presence of Z-VAD (100 µM) only for 48 h and analyzed by hematoxylin and eosin staining. At E14.5, medial edge epithelium periderm was retained in the atRA-treated palates but had been shed prior to contact in the control groups. In addition, atRA was revealed to disrupt the cell cycle in the periderm by downregulating p21. Furthermore, atRA inhibited apoptosis in the periderm and basal MEE cells; however, atRA exhibited no effect on basement membrane degradation in single palatal organ culture. Additionally, once paired palates were cultured for 48 h, all of the groups in which the periderm had been removed exhibited confluence of the embryonic palatal mesenchyme. The present results suggest that periderm removal is inhibited in atRA-induced cleft palate in mice and that removal of the periderm contributes to EPM confluence in vitro.