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Recently, the possibility of tooth tissue engineering has been reported. Although there are a number of available materials, information about scaffolds for tooth tissue engineering is still limited. To improve the manageability of tooth tissue engineering, the effect of scaffolds on in vivo tooth regeneration was evaluated. Collagen and fibrin were selected for this study based on the biocompatibility to dental papilla-derived cells and the results were compared with those of polyglycolic acid (PGA) fiber and beta-tricalcium phosphate (beta-TCP) porous block, which are commonly used for tooth, dentin and bone tissue engineering. Isolated porcine tooth germ-derived cells were seeded onto one of those scaffolds and transplanted to the back of nude mice. Tooth bud-like structures were observed more frequently in collagen and fibrin gels than on PGA or beta-TCP, while the amount of hard tissue formation was less. The results showed that collagen and fibrin gel support the initial regeneration process of tooth buds possibly due to their ability to support the growth of epithelial and mesenchymal cells. On the other hand, maturation of tooth buds was difficult in fibrin and collagen gels, which may require other factors.