BACKGROUND: High HIV-1 incidence rates were reported among persons in fisherfolk communities (FFC) in Uganda who were selected for high risk behaviour. We assessed the incidence of HIV-1 and associated risk factors in a general population FFC to determine population-wide HIV rates. METHODS: A community-based cohort study was conducted among a random sample of 2191 participants aged 18-49 years. At baseline and 12 months post-baseline, data were collected on socio-demographic characteristics and risky behaviors (including number of partners, new partners, condom use, use of alcohol and illicit drug use). Venous blood was collected for HIV serological testing. HIV incidence was calculated per 100 person years at-risk (pyar) and adjusted incidence rate ratios (Adj.IRR) were estimated by multivariable Poisson regression. RESULTS: Overall follow up at 12 months was 76.9% (1685/2191) and was significantly higher among HIV uninfected persons and those with at least 1 year duration of stay in community. Overall HIV-1 incidence was 3.39/100 pyar (95% CI: 2.55-4.49). Among the 25-29 years who drank alcohol, HIV incidence was 7.67/100 pyar (95% CI;4.62-12.7) while it was 5.67/100 pyar (95% CI;3.14-10.2) for 18-24 year olds who drank alcohol. The risk of HIV infection was higher among 25-29 years (adj.IRR = 3.36; 95% CI: 1.48-7.65) and 18-24 years (adj.IRR = 2.65; 95% CI: 1.05-6.70) relative to 30+ years. Compared to non-drinkers, HIV incidence increased by frequency of alcohol drinking--occasional drinkers (adj.IRR = 3.18; 95% CI: 1.18-8.57) and regular drinkers (adj.IRR = 4.93; 95% CI: 1.91-12.8). CONCLUSION: HIV-1 incidence in general fisherfolk population along L. Victoria, Uganda, is high and is mainly associated with young age and alcohol drinking. HIV prevention and control strategies are urgently needed in this population.