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The purpose of this study was to evaluate the implementation of a treatment protocol based on artemisinin-based combination therapy for the treatment of uncomplicated malaria in rural areas. Population and methods. A descriptive and comparative study was conducted in the rural health district of Houndé (Burkina Faso). The study involved health care providers, managers of essential drug depots and health centers, and patients receiving a prescription for an antimalarial drug. The data were entered and analyzed using the Epi Info 3.3.1 software package. The Chi-square test was used to compare proportions at the 0.05 level. A total of 130 prescribers and 30 managers of essential drug depots were interviewed in 28 health centers. In addition, 165 prescriptions including an antimalarial drug were collected. Of the 130 prescribers surveyed, 84.6% knew about the new treatment guidelines for uncomplicated malaria. The study found that 64.8% of the prescriptions were for ACTs, while quinine accounted for 35.2% of the prescriptions. Artesunate-amodiaquine combination therapy accounted for 98.1% of the prescriptions for antimalarial drug combination therapy. 82.4% of the prescriptions were adequate, with significantly more adequate prescriptions in clinics than in maternity hospitals (p = 0.009). Children under 5 years of age were treated better than other age groups (p < 0.001). In 89.7% of drug depots, there was evidence of a shortage of artemisinin-based combination drugs at least once in the two months before the study, most notably in the case of artesunate-amodiaquine therapy. The results highlight the importance of continuing training for treatment providers and of strict procedures for managing stocks of artemisinin-based combination drugs.