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Fluoride can alter the formation of mineralized tissues, including enamel, dentin, and bone. Dentin fluorosis occurs in tandem with enamel fluorosis. However, the pathogenesis of dentin fluorosis and its mechanisms are poorly understood. In this study, we report the effects of fluoride on the initiation of dentin matrix formation and odontoblast function. Mice from two enamel fluorosis susceptible strains (A/J and C57BL/6J) were given either 0 or 50 ppm fluoride in drinking water for 4 weeks. In both mouse strains, there was no overall change in dentin thickness, but fluoride treatment resulted in a significant increase in the thickness of the predentin layer. The lightly mineralized layer (LL), which lies at the border between predentin and fully mineralized dentin and is associated with dentin phosphoprotein (DPP), was absent in fluoride exposed mice. Consistent with a possible reduction of DPP, fluoride-treated mice showed reduced immunostaining for dentin sialoprotein (DSP). Fluoride reduced RUNX2, the transcription regulator of dentin sialophosphoprotein (DSPP), that is cleaved to form both DPP and DSP. In fluoride-treated mouse odontoblasts, the effect of fluoride was further seen in the upstream of RUNX2 as the reduced nuclear translocation of β-catenin and phosphorylated p65/NFκB. In vitro, MD10-F2 pre-odontoblast cells showed inhibition of the Dspp mRNA level in the presence of 10 μM fluoride, and qPCR analysis showed a significantly downregulated level of mRNAs for RUNX2, β-catenin, and Wnt10b. These findings indicate that in mice, systemic exposure to excess fluoride resulted in reduced Wnt/β-catenin signaling in differentiating odontoblasts to downregulate DSPP production via RUNX2.