OBJECTIVE: Chronic periodontitis (CP) is a common inflammatory disease that may cause systemic conditions. This study aimed to explore the correlation between serum Sirtuin 6 (SIRT6) levels and clinical characteristics of CP and the mechanism by which SIRT6 regulates osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs). METHODS: The serum expression of SIRT6 and enhancer of zeste homolog 2 (EZH2) in CP patients and healthy controls was measured by real-time quantitative polymerase chain reaction. The correlation between SIRT6 expression, clinical characteristics of CP [probing pocket depth/attachment level/bleeding on probing (PD/AL/BOP)], and EZH2 expression was assessed by Pearson analysis. hPDLSCs were cultured in adipogenic and osteogenic induction media, followed by measurement of adipogenic and osteogenic differentiation abilities. The levels of proinflammatory factors and cell viability in lipopolysaccharide-treated hPDLSCs were measured. After osteogenic induction of hPDLSCs, SIRT6 and EZH2 levels were detected. The enrichment of SIRT6 and H3K9ac on the EZH2 promoter was examined. RESULTS: SIRT6 was decreased in CP patients. SIRT6 expression was negatively correlated with PD/AL/BOP in CP patients and EZH2 expression. In the inflammatory microenvironment, osteogenic differentiation of hPDLSCs was suppressed, and SIRT6 expression was decreased. SIRT6 overexpression promoted osteogenic differentiation of hPDLSCs and alleviated inflammation. SIRT6 suppressed EZH2 expression by deacetylating H3K9ac. Overexpression of EZH2 partially reversed the promotive effect of SIRT6 overexpression on osteogenic differentiation of hPDLSCs under the inflammatory microenvironment. CONCLUSIONS: SIRT6 is negatively correlated with clinical characteristics of CP. SIRT6 is downregulated in hPDLSCs under the inflammatory microenvironment, and overexpression of SIRT6 promotes osteogenic differentiation of hPDLSCs by suppressing EZH2 expression through deacetylation of H3K9ac.