The enamel organ engaged in enamel matrix formation in tooth germs comprises four different cell types: the ameloblasts, the cells of the stratum intermedium, stellate reticulum, and the outer enamel epithelium, each characterized by distinct structural features. In ordinary primary cultures of tooth-derived cells, these cells generally become flat in profile and hardly regain their original profiles comparable to those in vivo, even under conditions that can induce the expression of functional markers from these cells. To overcome this limitation inherent to the cell culture of tooth-derived cells, we introduced a novel co-culture method, a “three-dimensional and layered (TDL) culture”, a three-dimensional (3D) culture of dental pulp-derived cells dispersed in type I collagen gel combined with a layered culture of enamel epithelial cells seeded on top of the gel to establish thereby a culture condition where the functional tooth-derived cells regain their original structures and spatial arrangements. We subjected the TDL gels thus prepared to floating cultures and found that, in the layered epithelial cells, those facing the 3D gel became cuboidal/short columnar in shape, showed cell polarity and well-developed intercellular junctions, had PAS positive material in their cytoplasm, and expressed a distinct immunoreactivity for cyotokeratin 14 and amelogenins. Pulpal cells in the gel displayed a strong ALP activity throughout the 3D gel. The current observations have clearly shown that the structural and functional features reminiscent of early secretory ameloblasts could be restored in the enamel organ-derived cells in a TDL culture.