The present study was designed to investigate the direct role of Shh molecule on cytodifferentiation and cusp formation. Affi-gel blue beads soaked in exogenous Shh-N, Shh antibody or BSA control protein were implanted between the epithelium and mesenchyme of isolated molar germs at the cap stage. The recombinants were grafted for culture under the kidney capsules respectively. In compared to the control, additional Shh-N protein could not enhance the ameloblasts and odontoblasts differentiation of the explanted tooth germs. While, application of Shh antibody retarded these events. After 4 weeks of subrenal culture, the teeth dissected from the explants treated with Shh-N were multicuspid. Most of the teeth harvested from the Shh antibody group were small and single irregularly shaped cusp was visible. The main cusp height in this group was reduced. The results indicated Shh signaling pathway is critical for odontoblast and ameloblast differentiation and patterns cusp formation.