| Summary: | Abstract Background To strengthen the fight against malaria, it is imperative to identify weaknesses and possible solutions in order to improve programmes implementation. This study reports experiences gained from collaboration between decision-makers and researchers from a World Bank project (Malaria and Neglected Tropical Diseases in the Sahel, SM/NTD). The objectives of this paper were to identify bottlenecks in malaria programme implementation as well as related research questions they bring up. Methods Questionnaire addressed to National Malaria Control Programme managers and prioritization workshops were used as a medium to identify research questions. The bottlenecks in malaria programme implementation were identified in seven thematic areas namely governance, human resources, drugs, service provision, use of prevention methods, monitoring and evaluation (M and E), and public support or buy-in. The first five priority questions were: (1) compliance with drug doses on the second and third days during the seasonal chemoprevention (SMC) campaigns, (2) the contribution of community-based distributors to the management of severe cases of malaria in children under 5 years, (3) the SMC efficacy, (4) artemisinin-based combination therapy (ACT) tolerance and efficacy according to existing guidelines, and (5) the quality of malaria control at all levels of the health system. Results and conclusion This work showed the effectiveness of collaboration between implementers, programmes managers, and researchers in identifying research questions. The responses to these identified research questions of this study may contribute to improving the implementation of malaria control programmes across African countries.
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