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Background: HIV and hepatitis B virus (HBV) co-infected patients have a significantly increased risk of dying from liver disease especially after starting treatment with highly active antiretroviral therapy. We aim to determine the prevalence of hepatitis B surface antigenaemia in HIV-infected children and their significance in relation to hepatic functions., Method: Two hundred and eighty four HIV-infected children aged between 4 mouths to 15 years attending the Paediatric infectious disease clinic of University of Maiduguri Teaching Hospital (UMTH) Maiduguri, Nigeria from September 2007 to December 2007 were the subject for this study. Two hundred and seventy six HIV-negative children with served as age and sex-matched controls. They underwent investigations to evaluate the liver function (serum alanine transferase (ALT), alkaline phosphotase (ALP) and bilirubin) and the prevalence of hepatitis B surface antigen (HBsAg) using ELISA technique., Results: Prevalence of HBsAg of 19% and 9.4% was observed among HIV-infected children controls (p = 0.004). Serum ALT and bilirubin concentrations were significantly higher in the HIV-infected group compared to the controls, (p < 0.05). HIV-infected children with HBs antigenaemia had significantly higher ALT and ALP concentrations compared to those without HBs antigenaemia (p < 0.05)., Conclusion: These findings point to the high risk of HBV infection and continual paranchymal damage in HIV-infected children before commencing ART. Vaccination against HBV should eliminate this risk. Ideally HBV serology should be evaluated before starting ART to help guide therapeutic decision-making.