Background: Human Immunodeficiency Virus/ Hepatitis B Virus (HIV/HBV) co-infection in Nigerian children has emerged as a major concern with the advent of HAART. Its impact on the immune system and liver has not been extensively studied in children. Objectives: To determine the prevalence of HBV seropositivity among HIV positive children on HAART and its effect on immune response and liver enzymes. Methods: All consecutive HIV positive children aged two months to seventeen years on HAART constituted the study population. Age and gender; CD4+ count, ALT, creatinine and HBsAg were tested and documented at enrolment and 12months. Results: One hundred and seventy one patients were seen over this period. Seventy-two (43.4%) were males while 94 (56.6%) were females giving a male: female ratio of 1:1.3. The mean age of the patients was 63±43.4 months. Prevalence of HIV/HBV co-infection was 6.02% (95% CI 2.4-9.7). There was no significant effect of HBV status on elevation of ALT levels with 12 months of HAART. Co-infected patients had an odds ratio of achieving immune response of 0.14 (95% CI 0.02-0.79). Conclusion: HIV/HBV co-infection rates in our children are comparable to other localities. ALT levels do not worsen with HAART and immune response of the co-infected children on HAART is lower. African Health Sciences 2013; 13(4): 955 -961 http://dx