INTRODUCTION: People living in fishing communities around Lake Victoria may be suitable for enrolment in HIV prevention trials because of high HIV incidence. We assessed the ability to recruit and retain individuals from fishing communities into an HIV vaccine preparedness cohort study in Masaka, Uganda. METHODS: HIV high risk, sero-negative adults (18-49 years) were identified from four fishing villages bordering Lake Victoria through door-to-door HIV counselling and testing (HCT). Interested persons were referred for screening, enrolment, and quarterly follow-up visits at a study clinic located approximately 30-40 kilometres away. Repeat HCT, HIV risk assessment, and evaluation and treatment for sexually transmitted infections were provided. Rates of and factors associated with study dropout were assessed using Poisson regression models. RESULTS: A total of 940 participants were screened between January 2012 and February 2015, of whom 654 were considered for the analysis. Over a two-year follow-up period, 197 (30.1%) participants dropped out of the study over 778.9 person-years, a dropout rate of 25.3 / 100 person-years of observation. Dropout was associated with being female (aRR = 1.56, 95% confidence interval [CI] 1.12-2.18), being 18-24 years (aRR = 1.64; 95% CI 1.03-2.60) or being 25-34 years (aRR = 1.63; 95% CI 1.04-2.55) compared to being 35+ years; having no education (aRR = 2.02; 95% CI: 1.23-3.31); living in the community for less than one year (aRR = 2.22; 95% CI: 1.46-3.38), or 1-5 years (aRR = 1.68; 95% CI: 1.16-2.45), compared to more than five years. CONCLUSIONS: Our results suggest that individuals from fishing communities can be recruited and retained in longitudinal studies; however, intensified participant tracing may be necessary for women, younger volunteers, those who are less educated and new residents.