Objective. As sub-Saharan Africa is highly endemic for hepatitis B virus (HBV) and human immunodeficiency virus (HIV) infections, and their co-infection requires special management, we aimed to assess the serological and molecular characteristics of HBV in patients with AIDS. Design. This was a cross-sectional, case control study, which enrolled 200 patients with AIDS and 200 HIV-negative controls. HBV serology was done in all participants and HCV serology in participants with a hepatitis B core antibody (anti-HBc) only serological pattern. Nested HBV polymerase chain reaction (PCR) and HBV viral load assays were used for HBV molecular detection. Results. Hepatitis B surface antigen (HBsAg) prevalence was 3-fold higher while the 'anti-HBc only' pattern was 6-fold higher in the AIDS group compared with the controls. Mean HBV viral load was significantly higher in HBsAg-positive patients with CD4+ cell counts <100 cells/μl than in patients with CD4+ cell counts of 100-200 cells/μl (p=0.019). There were markedly reduced hepatitis B surface antibody (anti-HBs) titres in the AIDS group compared with the controls (p=0.002). A significant proportion of AIDS patients with an 'anti-HBc only' pattern had CD4+ cell counts <100 cells/μl (p=0.004). Occult HBV prevalence was 3.5% in the AIDS group compared with 1% in the controls (p=0.092). When occult HBV infection was taken into consideration, the overall HBV prevalence became 10% in the AIDS group and 3% in the control group. Conclusion. We showed an increased HBV prevalence in patients with AIDS and identified a CD4+ cell count <100 cells/μl as a major risk factor for the 'anti-HBc only' pattern and increased HBV replication. These data have significant public health implications for HBV in developing countries, especially in areas where antiretroviral (ARV) guidelines do not cater for HBV/HIV co-infection.