Periodontitis leads to destruction of periodontal ligament, cementum and alveolar bone. Regeneration of periodontal tissue is dependent on mesenchymal stem cells (MSC) present in the periodontal ligament, and transcription factors determine the direction of MSC differentiation. The present study was conducted to investigate the transcription factors that are crucial for maintaining the characteristics of the periodontal ligament. The mRNA levels of several transcription factors were measured in cultured human periodontal ligament (HPDL) cells, human gingival fibroblasts and osteoblast-like Saos2 cells. HPDL cells were transfected for 72 h with siTwist2, siKlf12, or siMix (siTwist2, siPax9, and siKlf12). The cells were then harvested and subjected to real-time PCR and Western blotting. siTwist2 suppressed the levels of Twist2, Sox2 and Col1a1 mRNAs, and increased those of Sox5 and aggrecan mRNAs. siKlfl2 decreased the mRNA levels of Klf12, Runx3, Zfp521, and Stab2, and increased those of Sox2, Klf4, and the MSC markers CD90 and CD105. These results suggest that transfection with siMix and siTwist2 induced chondrogenesis, and that siKlfl2 induced the differentiation of MSC in 111)D1, cells. Thus, inhibition of Twist2 or Klf12 induced the differentiation of chondrogenic or mesenchymal stem cells in this setting, suggesting that the characteristics of HPDL cells may be altered by inhibition of specific transcription factors.