Moutan Cortex Radicis (MCR), the root bark of Paeonia suffruticosa Andrews (Paeoniaceae), is found in the traditional Chinese medicinal formulae which were used to treat periodontal diseases. This study investigated the changes in gene expression by MCR treatment when stimulated with lipopolysaccharide (LPS) in cultured human gingival fibroblasts (HGFs). A genome-wide expression GeneChip was used for the gene array analysis, and real-time reverse transcription polymerase chain reaction (RT-PCR) analysis was also performed to confirm the gene expression. It was shown that 42 of the 643 genes up-regulated by LPS, when compared to the control, were down-regulated by the MCR treatment. Of these 42 genes, the inflammation and immune response-related genes were especially noted, which indicates that MCR inhibits the induction of inflammation by LPS stimulation. In addition, 33 of the 519 genes down-regulated by LPS, when compared to the control, were up-regulated by the MCR treatment. The expression patterns of some representative genes by real-time RT-PCR correlated with those of the genes shown in the microarray. In addition, the MCR extract contained paeonol and paeoniflorin, which are known to have the anti-inflammatory effect as the major phenolic components of MCR. This study showed that the MCR extract could comprehensively inhibit a wide variety of activations of inflammation-related genes, which may be due to paeonol and paeoniflorin. It is, thus, suggested that MCR may be applied to alleviate the inflammation of periodontal diseases.