Background The conduct of longitudinal clinical trials must involve effective strategies to retain study participants in order to ensure internal validity, adequate statistical power and generalizability of results. Purpose In a large trial in Peru, we implemented various retention strategies to maintain high participation rates over time. Methods Novel participant retention strategies were used to follow highly marginalized populations for two years because traditional locator information, such as telephone numbers and official identification (eg, passport, driver's license, the local equivalent of a social security number) were often unreliable or unavailable. These strategies included detailed preliminary ethnographic research to identify the behaviours of key target groups, approaches to develop strong informal bonds between project staff and participants outside of study settings, and methods to enhance positive participant attitudes towards the study. Results The overall study retention rate after two years was 84%, even though only 26% of the study populations supplied complete locator information (telephone, address and the names of two friends). Limitations The retention strategies used were labour intensive and iterative, which could prove difficult to replicate. Conclusions The two-year retention rate in this study was sufficient to maintain required sample sizes. The methods used to maintain contact with the populations were labour intensive, low tech and adequate for these populations and could be used to retain study participants in other marginalized, urban, low-income areas.