Hepatitis B virus (HBV) and syphilis co-infections contribute significantly to HIV-associated morbidity and mortality, but the burden of these diseases is not fully appreciated in sub-Saharan Africa, as prevalence data are scarce. Both infections often remain undiagnosed in resource-limited settings because routine testing is not a part of most of the national guidelines. Epidemiological studies provide important information on prevalence and risk factors for such co-infections and can provide guidance for clinical management and for the development of test strategies. We analysed data on baseline characteristics, CD4 cell counts, HBV and syphilis co-infection rates of 690 patients enrolling for antiretroviral therapy in rural Cameroon. The prevalence of both hepatitis B surface antigen (HBsAg, 12.6%, 95% CI 10.1-15.1) and treponemal antibodies (11.4%, 95% CI 8.9-13.7) was high, with significantly higher prevalences for both infections in men; detection of treponemal antibodies increased with age. Although liver enzyme elevations were common, they were not useful to identify HBsAg-positive patients. In this setting, routine serological screening for HBV and syphilis co-infection should be considered to avoid complications and ongoing transmission.