Numerous studies have demonstrated the effect of shear stress on osteoblasts, but its effect on odontogenic cells has never been reported. In this study, we focused on the effect of shear stress on facilitating tissue-engineered odontogenesis by dissociated single cells. Cells were harvested from the porcine third molar tooth at the early stage of crown formation, and the isolated heterogeneous cells were seeded on a biodegradable polyglycolic acid fiber mesh. Then, cell-polymer constructs with and without exposure to shear stress were evaluated by in vitro and in vivo studies. In in vitro studies, the expression of both epithelial and mesenchymal odontogenic-related mRNAs was significantly enhanced by shear stress for 2 h. At 12 h after exposure to shear stress, the expression of amelogenin, bone sialoprotein and vimentin protein was significantly enhanced compared with that of control. Moreover, after 7 days, alkaline phosphatase activity exhibited a significant increase without any significant effect on cell proliferation in vitro. In vivo, enamel and dentin tissues formed after 15 weeks of in vivo implantation in constructs exposure to in vitro shear stress for 12 h. Such was not the case in controls. We concluded that shear stress facilitates odontogenic cell differentiation in vitro as well as the process of tooth tissue engineering in vivo.