Human dental follicle cells (DFCs) are progenitor cells. Recent studies supposed that osteogenic differentiation of DFCs is controlled by growth factors such as BMP2 and IGF2, but their influence on the differentiation of DFCs has not been investigated in detail. We examined DFCs after the induction of osteogenic differentiation with BMP2, IGF2 and a standard osteogenic differentiation medium (ODM) with dexamethasone. The alkaline phosphatase (ALP) activity and the calcium accumulation demonstrated osteogenic differentiation after all treatments, but with the most effective differentiation by ODM. Interestingly, markers of the process of osteoblast differentiation were much higher up-regulated in BMP2- or IGF2-treated cells than in ODM-treated cells. To evaluate the reason of these differences, we compared genome-wide expression profiles at an early stage of differentiation. Chondroblast markers in BMP2-differentiated cells and general markers for cell differentiation/proliferation in IGF2-treated cells were significantly regulated. However, ODM-treated DFCs expressed late markers of osteogenic-differentiated DFCs such as the transcription factor ZBTB16 that is not expressed in BMP2- or IGF2-differentiated cells. Importantly, although the BMP-antagonist noggin (NOG) diminishes the phosphorylation of SMAD1 in DFCs, it did not inhibit osteogenic differentiation by ODM and the expression of ZBTB16. In conclusion, this study demonstrates that osteogenic differentiation of DFCs can be stimulated with all tested inducers but also independently of BMP signaling. To evaluate this mechanism, the transcription factor ZBTB16 is a target for further investigations.