Periodontitis is an inflammatory disease, which destroys the connective tissue and the alveolar bone. Recently, it has been suggested that the effect of natural substances could be induced into an anti-inflammatory environment. However, the effect of Safflower seed extract (SAF-M) associated with periodontitis has not been investigated yet. Therefore, the purpose of this study was to assess the anti-inflammatory effects of SAF-M. Cytotoxicity was assessed through MTS analysis using hGF and hPDL cells. Periodontitis was induced by injecting LPS into gingival tissue on the maxillary molars of rats (45 μg LPS/one time, 3 times a week for 3 weeks). SAF-M was administered daily at 30 mg/kg and 100 mg/kg. Alveolar bone resorption was evaluated through the micro-CT. hGF and hPDL cells showed differential cytotoxicity in response to SAF-M at 5 mg/ml and 1 mg/ml concentrations. Micro-CT showed reduction of the alveolar bone resorption in the SAF-M treatment group. These results suggested that SAF-M is a potential therapeutic agent for periodontitis.