It has been proposed that occult hepatitis B virus (HBV) infection, defined as detectable HBV-DNA in serum with undetectable surface antigen (HBsAg(-)), is associated with raised transaminases in HIV-infected persons. The aim of this study was to determine the prevalence of occult HBV infection in two independent cohorts, and investigate its predictors, association with alanine-aminotransferase (ALT) levels and response to antiretroviral therapy. Sera from HBsAg(-) persons with core antibody (anti-HBc(+)) were tested by real-time PCR. Overall, 5.2% of patients were HBsAg(+) and 39% HBsAg(-)/anti-HBc(+). The prevalence of occult HBV infection was 48/343 (14.0%; 95% CI 10.7-18.1%), and 27/196 (13.8%) and 21/147 (14.3%) in the two cohorts. Median HBV-DNA load was 342 (51-147,500) and 60 (25-33,850) copies/ml respectively. HBV-DNA detection was associated with absence of surface antibody (anti-HBs), but not with CD4 or ALT levels. Among 11 HBV-DNA(+) persons who started antiretroviral therapy containing lamivudine or lamivudine/tenofovir, HBV-DNA was repeatedly undetectable over median 19 (3-43) months. However, HBV-DNA detection was intermittent among drug-naïve persons. Occult HBV infection is common in HBsAg(-)/anti-HBc(+) HIV-infected patients and predicted by undetectable anti-HBs. The intermittent nature of HBV-DNA detection poses a diagnostic challenge, but no association is observed with ALT levels.