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Background: In 2009, the Global Fund to Fight AIDS, Tuberculosis and Malaria established the Affordable Medicines Facility-malaria (AMFm) in order to increase access to quality-assured artemisinin combination therapy (QAACT). AMFm Phase 1, which includes nine pilot programmes in eight countries, was launched in 2009. The objective of this study was to assess anti-malarial stock and purchase patterns at private outlets in five AMFm Phase 1 countries in regard to three of the core AMFm goals: increase the affordability of QAACT, increase the availability of QAACT, and crowd out artemisinin monotherapies and other substandard therapies., Methods: The study was conducted between April and May 2012 and included interviews with personnel in 598 private pharmaceutical outlets in Ghana, Kenya, Nigeria, Tanzania, and Uganda. Questionnaires were administered at private retail outlets and the data were analyzed to assess within- and between-country differences in QAACT price, availability, and popularity., Results: AMFm medications were less expensive than their non-AMFm counterparts, yet prices for both types were above country-specific suggested retail prices. Market penetration of AMFm QAACT in both urban and rural areas was high, although stock-outs of both AMFm and non-AMFm products were more common in rural compared with urban outlets in Ghana and Kenya (p = 0.0013). Government recommendation was the most significant factor influencing anti-malarial stock choices in urban (41.5%) and rural (31.9%) outlets. The three top-selling anti-malarials reported for both urban and rural areas in each country were, with the exception of rural Uganda and urban Nigeria, combination therapies., Conclusions: Results from this study indicate that the AMFm has not fully achieved its affordability and crowd-out objectives. Still, the final purchase price of AMFm QAACT was substantially lower than non-AMFm equivalents. Moreover, for both urban and rural areas, AMFm QAACT availability was found to be high, and the various forms of QAACT were the best-selling products among all anti-malarials. These findings suggest a continued need for initiatives like the AMFm that improve the affordability and accessibility of QAACT. Similar programmes may be especially effective if employed in combination with rapid diagnostic testing to ensure the appropriate use of these products.