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Objective To determine the effect of the Affordable Medicines Facility for malaria (AMFm) launched in April 2011 in Uganda on the use of Artemisinin Combination Therapies (ACTs) for malaria treatment.Methods 2398 households across six districts in Eastern Uganda were monitored through monthly survey visits from April 2011 to April 2012. During each visit, health seeking modules were completed for any morbidity episode reported by the household. Additional surveys were conducted with 114 licensed drug shops in the same districts in April 2011 and April 2012. Changes in drug shops’ stocking and pricing of ACTs, as well as changes in households’ treatment behaviour and drug usage were analysed.Results The fraction of licensed drug shops reporting that an ACT was one of their top five bestselling antimalarial drugs increased from 32% to 84% (Δ = 0.517, 95% Confidence Intervals (CI) [0.407, 0.628], P < 0.001). The fraction of children under the age of 5 with fevers getting an ACT increased from 37% to 47% (Δ = 0.103, 95% CI [0.070, 0.136], P < 0.001), and the fraction of ACT treatments among patients getting any antimalarial increased from 51% to 65% (Δ = 0.145, 95% CI [0.121, 0.169], P < 0.001). The observed changes were particularly large among poorer households, and were smallest for households from the highest wealth quintile.Conclusions The study results suggest that, during its first year of implementation in Uganda, the AMFm achieved its main objective of increasing the availability and use of ACTs. Estimates of the impact of the AMFm on ACT use for children under 5 imply that the program should be considered highly cost-effective under current World Health Organization (WHO) guidelines. The overall results look promising, but larger and longer term studies will be needed to assess the health impact and cost-effectiveness of the program.