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Presumptive treatment of malaria results in significant overuse of antimalarials. Malaria rapid diagnostic tests (RDTs) may offer a reliable alternative for case management, but the optimal RDT strategy is uncertain. We compared the diagnostic accuracy of histidine-rich protein 2 (HRP2)- and plasmodium lactate dehydrogenase (pLDH)-based RDTs, using expert microscopy as the gold standard, in a longitudinal study of 918 fever episodes over an 8-month period in a cohort of children in Kampala, Uganda. Sensitivity was 92% for HRP2 and 85% for pLDH, with differences primarily due to better detection with HRP2 at low parasite densities. Specificity was 93% for HRP2 and 100% for pLDH, with differences primarily due to rapid clearance of pLDH antigenemia after treatment of a previous malaria episode. RDTs may provide an effective strategy for improving rational delivery of antimalarial therapy; in Kampala, either test could dramatically decrease inappropriate presumptive treatments.