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Background: High retention (follow-up) rates improve the validity and statistical power of outcomes in longitudinal studies and the effectiveness of programs with prolonged administration of interventions. We assessed participant retention in a potential HIV vaccine trials population of fishing communities along Lake Victoria, Uganda., Methods: In a community-based individual randomized trial, 662 participants aged 15-49 years were randomized to either mobile phone or physical contact tracing reminders and followed up at months 1, 2, 3, 6, 12 and 18 post-enrolment. The visit schedules aimed at mimicking a vaccine efficacy trial representing an early interval (months 1-6) where most vaccinations would be administered and a later period of post-vaccination follow-up. The primary outcome was retention measured as the proportion of post-baseline follow up visits completed by a participant. Retention was estimated in early and later follow-up intervals, and overall for all the six follow-up visits. Adjusted differences in retention between the study arms were determined by multivariable logistic regression using Stata® 14. One participant was later dropped from the analysis because of age ineligibility discovered after enrolment., Results: Of the expected total follow up visits of 3966 among 661 participants, 84.1% (3334) were attained; 82.1% (1626/1980) in the phone arm and 86% (1708/1986) in the physical tracing arm (p = 0.001). No statistically significant differences in retention were observed between the study arms in the first 6 months but thereafter, retention was significantly higher for physical contact reminders than mobile phones; 91.5% versus 82.1% (p < 0.0001) at month 12 and 82.8% versus 75.4%, (p = 0.021) at month 18. Controlling for sex, age, education, occupation, community location, length of stay and marital status, the odds of good retention (completing 5 out of 6 follow-up visits) were 1.56 (95% CI;1.08-2.26, p = 0.018) for physical contact tracing compared to mobile phone tracing. Other statistically significant predictors of good retention were residing on islands and having stayed in the fishing communities for 5 or more years., Conclusions: Among fishing communities of Lake Victoria, Uganda, 84% of follow-up visits can be attained and participant retention is higher using physical contact reminders than mobile phones., Trial Registration Number: PACTR201311000696101 ( http://www.pactr.org/ ). retrospectively registered on 05 November, 2013.