The invention provides methods, apparatus and kits for regenerating dental tissue in vivo that are useful for treating a variety of dental conditions, exemplified by treatment of caries. The invention uses tissue scaffold wafers, preferably made of PGA, PLLA, PDLLA or PLGA dimensioned to fit into a hole of corresponding sized drilled into the tooth of subject to expose dental pulp in vivo. In certain embodiments the tissue scaffold wafer further comprises calcium phosphate and fluoride. The tissue scaffold wafer may be secured into the hole with a hydrogel, a cement or other suitable material. Either the wafer or the hydrogel or both contain a morphogenic agent, such as a member encoded by the TGF-.beta. supergene family, that promotes regeneration and differentiation of healthy dental tissue in vivo, which in turn leads to remineralization of dentin and enamel. The tissue scaffold may further include an antibiotic or anti-inflammatory agent.