In tooth eruptions, the presence of apoptotic epithelial cells at the eruption site has been reported, but the factors that induce apoptosis in these cells remain to be elucidated, as do the induction pathways. In this study, we focused our attention on transforming growth factor beta (TGF-beta), which is known to induce apoptosis during embryonic development. Oral epithelium and dental lamina of maxillary first molars in 8- and 15-day-old rats were used to investigate the induction pathway of apoptosis by performing the immunohistochemical tests outlined below and assessing the characteristics of cells that undergo apoptosis by transmission electron microscopy in rats 8 and 15 days after birth. We examined TGF-beta-receptor 1, TGF-beta inducible transcription factor 1 (TIEG1), NADPHoxidase 4 (Nox4), cytochrome c, caspase-3 (active form and pro-enzyme), apoptosis-inducing protein Daxx, apoptosis signal-regulating kinase 1 (ASK1), glycogen synthase kinase-3 beta phosphorylated on serine 9 (p-GSK-3beta), and beta-catenin. We also performed periodic acid Schiff (PAS) reaction and terminal deoxynucleotidyl transferase-mediated dUTD nick end labeling (TUNEL) staining. At eruption sites 8 days after birth, reactions to TGF-beta-receptor 1, TIEG1, Nox4, cytochrome c, caspase-3, p-GSK-3beta, and beta-catenin, and PAS-positive cells were observed in areas close to the basal layer of oral epithelium through to the center of the dental lamina, but no reaction to Daxx or ASK1 was noted at these sites. Electron microscopy revealed the accumulation of glycogen granules in the cells that showed reactions to the above-mentioned markers as well as in the spaces among them. In the rats 15 days after birth (immediately before tooth eruption), the PAS-positive cells that showed reactions to the above antibodies remained on the buccal side of the epithelium, and high-electron-density apoptotic bodies and TUNEL-positive bodies were noted. Therefore, during tooth eruption, TGF-beta may induce apoptosis of cells rich in glycogen granules, and cytochrome c and caspase-3 may function to induce apoptosis. In addition, reactive oxygen species may be involved in this induction pathway via TIEG1 and Nox4 without involvement of Daxx and ASK1. Moreover, overexpression of p-GSK-3beta and beta-catenin may also contribute to apoptosis of oral epithelium at the eruption site and dental lamina cells. Glycogen storage mediated by p-GSK-3beta and crosstalk between the TGF-beta and Wnt signaling pathways may participate in the formation of tooth eruption passage.