Hepatitis B virus (HBV), Hepatitis C virus (HCV) and Human Immune Deficiency virus (HIV) are among the top 10 leading causes of infectious diseases deaths worldwide.Viral hepatitis is common in the tropics including Nigeria where it is a major cause of both acute and chronic liver diseases.Since these organisms share similar routes of transmission; persons at high risk for HIV infection are also likely to be at risk for other blood borne infectious pathogens, including HBV and HCV.The aim of this study was to determine the epidemiology of hepatitis B and hepatitis C virus infection among HIV Counseling and Testing (HCT) clients at the Jos University Teaching Hospital (JUTH), Nigeria from November, 2012 to April 2013. This was done bycollecting demographic data, exposure to associated factors and laboratory determination of HBV and HCV sero-prevalence in the subjects using ELISA and PCR assay methods. The demographic characteristics of 232 HCT subjects were analysed; 132(56.9%) of them were females while 100 (43.1%) were males. In response to the questionnaire administered, there were no statistically significant factors associated with exposure to HBV or HCV in these subjects. Among the subjects studied, 36 (15.5%) tested positive for HBsAg by ELISA, 31 (13.4%) subjects were confirmed positive by DNA PCR giving rise to a concordance rate of 86.1%. Among the subjects 9(3.9%) tested positive by ELISA to HCV antibody, out of this 7 (3.0%) were confirmed positive by RNA PCR, this gives a concordance rate of 77.8%. There was no HBV/HCV, HIV/HCV and HIV/HBV/HCV co-infection among the subjects studied. The co-infection rate of HIV / HBV in HCT subjects was 5.2%. This study concluded that, the prevalence of HBV and HCV infection by 2 ELISA and by DNA PCR among HCT clients in Jos University Teaching Hospital was high. The infection was substantial among the study population especially in those younger than 37 years in the case of HBV and those older than 36 years in the case of HCV. Co-infection rate of HIV/ HBV in the population was significant. No other coinfection was elicited. Specific demographic factors associated with exposure to HBV and HCV infection in Jos from this study were not statistically significant; to determine this would call for a larger population group study instead of a health facility based study. It is recommended that, Promotion of HBV vaccination in the general population and continuation of HBV vaccination of children as part of the expanded programme on immunization should be encouraged. Healthcare workers and all persons taking up work in a health care environment like undergraduate medical students, Nursing and Laboratory students should be tested and vaccinated against HBV. Hospital authorities should make available molecular biology laboratories to Physicians for the diagnosis and more effective monitoring of these viral and other infectious diseases. It is only the use of PCR in screening that would identify infected subjects in their window period; this has implications for blood transfusion and tissue transplant services.Viral load should be used to monitor patients in the management of HBV, HCV and HIV infected patients. This study was limited by the fact that the design was cross sectional - a direct observation of the sero-prevalence of HBsAg and HCV only; the implication of the effect of one virus over the other was not deduced.