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This study aims to investigate the associations of hypomethylation and over expression of the TLR9 gene with systemic lupus erythematosus (SLE). Fifteen SLE patients who were diagnosed and not treated, were selected as cases, and 32 healthy subjects were enrolled as controls. DNA and total RNA of peripheral blood mononuclear cells (PBMCs) were extracted. The methylation status of the promoter region CpG motifs of the TLR9 gene was quantitatively measured using bisulfite sequencing PCR, and the mRNA expression of the TLR9 gene was determined using realtime fluorescent quantitative PCR. The methylation level of the 10 TLR9 CpG motifs of gene did not show difference between cases and controls (P>0.05). By contrast, we observed an abnormal increase of TLT9 mRNA expression in patients (P=9.379×10-8), which was significantly correlated with SLEDAI (Systemic Lupus Erythematosus Disease Activity Index) (P=9.018×10-7). The change of TLR9 gene expression may play an important role in the pathogenesis of SLE. [ABSTRACT FROM AUTHOR]