Focus groups were conducted with 100 secondary school and college students in Kanungu, Uganda in 2011. Three parallel groups considered HIV, malaria and family planning, and common messages were then explored jointly in a workshop based on the RE-AIM framework (Reach, Effectiveness, Adoption, Implementation and Maintenance). Results Participants identified various reasons why preventive action was not always taken. They worried about the effectiveness and side effects of several key interventions: condoms, antiretroviral treatment, various contraceptives and impregnated mosquito nets. Cost, rural isolation and the quality and availability of health services also limited the extent to which people were able to follow health advice. Although there was respect for policy supporting abstinence and fidelity, it was seen as hard to follow and offering inadequate protection when gender imbalance put pressure on women to have sex. Conclusions There is an opportunity to improve the uptake of preventive measures by tackling the misconceptions and fears that participants reported with clear, evidence-based messages. This should be done in a way that encourages more open communication about reproductive health between men and women, that reaches out to isolated communities, that draws on both voluntary