Nigeria has the largest burden of children living with HIV in the world but because of antiretroviral therapy, they are living longer. However, hepatitis B and C viruses are emerging important co-morbidities to consider especially for management decisions. This study set out to determine the prevalence of hepatitis B and C viruses among these children and to identify possible risk factors associated with the infections. Two hundred HIV-infected children at an antiretroviral treatment center were screened for Hepatitis B and C seromarkers using rapid test kits (ABCON Laboratories Hangzhou China). Informed written consent was obtained from their parents/guardian and information on their sociodemographics and exposure to some possible risk factors were obtained. A general prevalence of infection with hepatitis B and C virus in the study population was 14.0%. The prevalence of HBV was 3.0% while HCV was 11.0% and no child was coinfected with all 3 viruses. The HIV/HBV and HIV/HCV coinfection prevalence of 3.0% and 11.0% respectively is a cause for alarm. It is therefore pertinent that HIV infected children are screened for these viruses before commencement and during antiretroviral therapy.