To examine the expression of naked cuticle homolog 2 (Nkd2) in the process of root development and osteogenic differentiation of dental follicle cells of rat (rDFC), in order to explore the molecular mechanisms of Nkd2 on the osteoblast differentiation of rDFCs. Immunohistochemical analysis was used to detect the expression of Nkd2 in the base dental follicle of the mandibular first molar of rat at 1, 3, 5, 7, 9, 11 and 13 days postnatal. Mineralization nodule formation of rDFCs was detected by alizarin red staining and cetylpyridine. The change of Nkd2 during osteogenic differentiation of rDFCs was evaluated by Western blotting and the associations between Nkd2 and osteogenic cytokines of alkaline phosphatase (ALP), Runt-related transcription factor-2 (RUNX2) and osteocalcin (OCN) were examined. The rDFCs were transfected with small interfering RNA (siRNA) to knock down the expression of Nkd2 and Western blotting and quantitative real-time PCR (qPCR) were adopted to explore the effects of Nkd2 on osteogenic differentiation by detecting variations of Nkd2 and osteogenic factors ALP, RUNX2, OCN among silencing group (Si), negative control RNA group (Nc) and mock control group (Mock), respectively. The expression of Nkd2 in the base dental follicle of the mandibular first molar of rat was time dependent. Mineralization nodules of rDFCs and absorbance of cetylpyridine after osteogenic induction increased gradually (the absorbances of cetylpyridine were 0 week: 0.017±0.005, 1 week: 0.702±0.044, 2 weeks: 1.812±0.531, 3 weeks: 2.767±0.253, respectively). Results of Western blotting showed that Nkd2 (1.60±0.23) of mineralization group was significantly higher than that of control group (1) (0.05) at the early stage of osteogenic differentiation along with the expression of other osteogenic factors. The protein and mRNA of Nkd2 and osteogenic factors were significantly decreased in Si group compared with Nc and Mock groups (0.05), and no changes between Nc and Mock groups were observed. The changes of protein in Si, Nc and Mock groups were Nkd2: 0.42±0.10, 1.12±0.07, 1, ALP: 0.70±0.15, 1.11±0.14, 1, RUNX2: 0.58±0.08, 0.93±0.08, 1 and OCN: 0.64±0.06, 0.99±0.02, 1, respectively. The mRNA variances in Si, Nc and Mock groups were Nkd2: 0.39±0.05, 0.96±0.10, 1, ALP: 0.15±0.13, 1.01±0.07, 1, RUNX2: 0.39±0.31, 0.97±0.13, 1, OCN: 0.17±0.08, 1.08±0.21, 1, respectively. Nkd2 participates in the root development process in rat and may acts as a positive role in the early stage of osteogenic differentiation of rDFCs in rat.