The aim of the present study was to investigate the expression of toll-like receptors (TLR) 9 in peripheral blood mononuclear cells (PBMC) of patients with chronic hepatitis B and C with different virus copies. The study group included 90 patients (60 with chronic hepatitis B, and 30 with chronic hepatitis C), and 20 healthy people served as control group. The protein and mRNA levels of TLR9 were detected by using flow cytometry and real-time PCR. The serum viral copies of HBV and HCV were measured in all patients, and the correlation between HBV-DNA copies or HCV-RNA copies and the TLR9 expression was analyzed. Our results demonstrated that HBV or HCV infection led to a decreased expression of TLR9 mRNA and protein compared to the control group (P<0.05). The TLR9 protein and mRNA levels were negatively correlated with serum viral copies of HBV and HCV (r=-0.632, r=-0.909, P<0.01). It was concluded that TLR9 mRNA and protein are down-regulated in PBMC of HBV-infected or HCV-infected patients, and they are negatively correlated with serum viral copies and play an important role in detecting viral replication of HBV and HCV.