Background The characteristics associated with incident hepatitis B (HBV) infection in HIV-positive individuals are not well described in the Australian setting. The aim of this study is to determine the characteristics of and risk factors for HBV infection within HIV-infected individuals in a Melbourne cohort between 1985 and 2011. Methods: Individuals susceptible to HBV at their HIV diagnosis were identified using their HBV serology stored within the Victorian HIV database. Within this group, those who had a subsequent positive test for hepatitis B surface antigen or hepatitis B core antibody were identified as infected with HBV after their HIV diagnosis. Incident cases were matched with controls from the initially susceptible group who did not seroconvert for analysis. An incidence rate was calculated from the number of seroconversions and the cumulative time at risk (in 1000 patient-years of follow-up). Results: Of the 4711 patients with HIV seen more than once, 3223 had HBV testing. Of the 174 with positive HBV test results, 39 individuals met the definition of seroconversion after HIV diagnosis, representing the incident cases. The estimated HBV incidence rate was 1.81 (95 confidence interval: 1.28-2.47) per 1000 patient-years at risk. These individuals form the basis of a detailed case series and case-control study. Data collected include demographic details, immunological and virological characteristics, antiretroviral treatment and vaccination history. Conclusions: HIV-infected individuals should be screened for HBV and monitored for incident infection. Optimal control of HIV and improved vaccination coverage provide the best opportunity for prevention.