The incidence of HIV associated with medical injections was assessed in a cohort of 6868 HIV-negative individuals; 42.8% reported injections and 0.5% reported transfusions. The Poisson adjusted rate ratios and 95% confidence intervals (CI) of incident HIV were 1.05% (CI 0.75-1.46) associated with medical injections, and 3.92 (CI 1.22-12.58) associated with transfusions. Sexual behaviours were significantly associated with HIV risk. Medical injections did not increase HIV acquisition in this rural Ugandan population.