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Purpose: HIV, bacterial sepsis, malaria, and tuberculosis are important causes of disease in Africa. We aimed to determine the impact of HIV on the presentation, causes and outcome of bacterial sepsis and other acute febrile illnesses in Gabon, Central Africa., Methods: We performed a prospective observational study in new adult admissions with fever or hypothermia (≥ 38 or <36 °C). Blood cultures, as well as HIV and malaria testing were performed in all patients., Results: We enrolled 382 patients, including 77 (20.2%) with HIV infection. Malaria was the most frequent diagnosis (n = 130, 34%), and was associated with a more severe presentation in HIV patients. Sepsis was also common (n = 107, 28%), including 29 (7.6%) patients with culture confirmed bacterial bloodstream infection. Bacterial bloodstream infections were more frequent in HIV patients, in particular with S. pneumoniae. Tuberculosis was observed in 29 (7.6%) patients, and was also more common in HIV patients. The majority of HIV patients was newly diagnosed, and only 15 (19.5%) were using combination antiretroviral therapy., Conclusions: Our findings illustrate the impact of HIV co-infection on the burden of sepsis, malaria and tuberculosis in Gabon, as well as the need to scale up HIV counseling, testing and treatment.