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Abstract Objective To evaluate the prevalence of hepatitis C virus (HCV) infection in high risk juvenile systemic lupus erythematosus (JSLE). Study design Forty low income JSLE patients (6M:34F; mean age 19 ± 4.4 yrs; mean disease duration 6 ± 3.2 yrs) were studied. Twenty healthy children and adolescents matched for social economical level were included as controls. Anti-HCV tests were performed using a third generation microparticle enzyme immunoassay. Inclusion criterion was low social economical level. Results The frequencies of anti-HCV antibody were low and comparable between JSLE and control group (2.5% vs. 0, p = 1.0). JSLE patients had significantly more risk factors for HCV infection compared to the control group, including immunosuppressive treatment (90% vs. 0, p < 0.0001), hospitalization (50% vs. 12.5%, p = 0.0006) and invasive procedures (47.5% vs. 12.5%, p = 0.001). Conclusions The observed low frequency of anti-HCV antibodies in high risk JSLE suggests that this virus does not seem to have a relevant role in the pathogenesis of this disease.