There exists a close connection between changes occurring in the teeth and those occurring in the jaw during the evolutionary process. In mammals, the roots of teeth are supported, along with periodontal ligaments and alveolar bones by a unique structure termed the gomphosis. In the present study, we performed combined in silico analysis using the information obtained from various DNA microarrays and identified 19 putative tooth root formation-related genes. Furthermore, quantitative PCR was performed on the candidate genes, Chd3 was confirmed as having sufficient expression levels in the early stage of tooth root formation and increased gene expression toward the middle stage. A high degree of Chd3 gene expression was observed in secretory ameloblasts and Hertwig's epithelial root sheath (HERS), but low expression was observed in developing odontoblasts and stellate reticulum. The CHD3 foci were observed in the nucleus of the HERS01a cells. In addition, knockdown experiments using SiChd3 suggested the involvement of Chd3 in the suppression of DNA synthesis. These results suggested that Chd3 plays a role in DNA synthesis in HERS cells for promoting tooth root development.