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Background: Artemisinin-based combination therapies (ACTs) have proven highly effective in reducing malaria morbidity in sub-Saharan Africa. Artemether-lumefantrine (AL) was introduced in 2005 as a first-line ACT for the treatment of uncomplicated malaria in Rwanda. Monitoring the therapeutic efficacy of ACTs is necessary to ensure effective malaria case management., Methods: A comparative study on the efficacy of AL and dihydroartemisinin-piperaquine (DHP) was conducted in two sites, Masaka and Ruhuha, between September 2013 and December 2015. Clinical and parasitological responses were assessed at days 28 and 42., Results: A total of 534 children were treated with AL (n=267) or DHP (n=267). After polymerase chain reaction (PCR) adjustment, 98.3% and 98.9% of children in the AL and DHP arms, respectively, achieved an adequate clinical and parasitological response (ACPR) at day 28. At day 42, PCR-adjusted ACPR proportions were 97.3% and 98.4% for AL and DHP, respectively. PCR-adjusted ACPR was 99% for both drugs at days 28 and 42 in Ruhuha. The PCR-adjusted ACPR proportions in Masaka were 97.3% for AL and 98.5% for DHP at day 28 and 95.2% for AL and 97.5% for DHP at day 42., Conclusions: AL remains efficacious in Rwanda 10 y after its adoption. The probability of new infections occurring among patients in the DHP arm was significantly lower than those in the AL arm. DHP also demonstrated a greater post-treatment prophylactic effect against new infections compared with AL., (© The Author(s) 2019. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)