Malaria is a major public health problem in Uganda. Current policy recommends introduction of rapid diagnostic tests (RDTs) to facilitate effective case management. However, provision of RDTs in drug shops raises new issues, such as adherence to RDTs results, management of severe illnesses, referral of patients, and relationship with caretakers. This study examine the impact of introducing RDTs in registered drug shops in Uganda to document lessons and policy implications for future scale-up in the private health sector. A cluster-randomized trial introducing RDTs into registered drug shops was implemented in central Uganda from October 2010 to July 2012, and then evaluated for lessons learned and policy implications. The study found that introducing RDTs into drug shops was feasible and it increased appropriate treatment of malaria with artemisinin-based combination therapy. It is anticipated that the lessons presented will help better implementation of similar interventions in the private sector.