Applying of 1.23% acidulated phosphate fluoride (APF) gel to prevent caries in children has become very popular among dental practitioners. When applied to dental surfaces, however, APF often comes into contact with the oral mucosa. Due to the possibility of local toxic effect, we aimed to investigate the effects of APF on rabbit oral mucosa. Rabbits were sacrificed 1, 5 and 8 days after topical application of 1.23% APF on the oral buccal mucosa for 4 min. The nuclei with DNA strand breaks of the basal epithelial cell layer was estimated using terminal-deoxynucleotidyl-transferase-mediated deoxyuridine-triphospate-biotin nick end labeling (TUNEL). Epithelial cells were analyzed by transmission electron microscopy. The number of basal epithelial cells with DNA strand breaks increased with time in rabbits treated with 1.23% APF. Transmission electron microscopy revealed evidence of apoptosis in the parabasal and basal epithelial cells showed, with loss of cell-to-cell contact, nuclear chromatin condensation and apoptotic bodies. The results demonstrate in vivo that 1.23% APF induced apoptosis in basal epithelial cells of rabbit oral mucosa. It suggests the possible necessity to prevent oral mucosa contact when APF applied on teeth.