Methods: Patients were selected from HIV infected children medically eligible for ART who were enrolled into the China national pediatric ART cohort since 2004. Interviews, medical assessment, serology for HBsAg, anti-HCV antibody, transaminase levels, and HIV serostatus and CD4 counts at baseline of patients were obtained. Results: 42 of 763 HIV-infected children were HBsAg seropositive (5.50%; 95%CI: 3.88%-7.12%), and 69 of 662 children were anti-HCV antibody seropositive (10.42%; 95%CI: 8.09%-12.75%). Only age was associated with HBV coinfection. Multivariate analysis revealed that children infected with HIV through contaminated blood or transfusion of blood products were 6.35 times more likely to be anti-HCV antibody positive than those infected with HIV through other routes. And children from central China provinces, Henan, Anhui, Shanxi, and Hubei were 2.5 times more likely to be HCV seropositive.