The current study assessed the association between toll-like receptor 9 (TLR9) and systemic lupus erythematosus (SLE) and subsequently determined the predictive value of TLR9 in assessing the prognosis of SLE. A total of 90 newly diagnosed patients with SLE and 49 healthy control subjects were enrolled in the current study. The expression of TLR9 mRNA was measured in whole blood samples from patients and controls. All patients were followed up for ≥2 years and their clinical parameters were recorded. After 2 years, 30 patients were randomly chosen from patient subgroups with high (n=20) or low (n=10) TLR9 levels and the expression of TLR9 mRNA were measured again. Cox proportional hazards regression was used to identify the risk factors of SLE prognosis. Patients with SLE and high SLE disease activity exhibited significantly increased TLR9 expression (P<0.05). Persistent proteinuria of >0.5 g/day [hazard ratio (HR), 6.314; 95% confidence interval (CI), 2.858-13.947], C-reactive protein levels (HR, 1.013; 95% CI, 1.007-1.019) and high-TLR9 mRNA expression (HR, 3.852; 95% CI, 1.931-7.684) were independent risk factors of poor prognosis during a 2-year follow-up period, whereas patient treatment with >1 immunosuppressant (HR, 0.374; 95% CI, 0.173-0.808) was a factor indicating favorable prognosis. Furthermore, the expression of TLR9 mRNA remained high in patients with poor prognosis at the end of a 2-year follow-up period but in patients with a favorable prognosis, TLR9 mRNA expression was significantly reduced compared with the levels measured at SLE onset (P<0.0001). Therefore, the expression of TLR9 mRNA in whole blood samples at SLE onset is associated with SLE disease activity and its expression may be used as an indicator of poor prognosis in patients with SLE.