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This paper describes the first African experience with the Nutrition-Friendly School Initiative (NFSI) in two large West African cities: Ouagadougou, Burkina Faso and Cotonou, Benin. NFSI was launched by the World Health Organization (WHO) and its partners in 2006, as a means of preventing the double burden of malnutrition: the coexistence of undernutrition and overnutrition among school-children. NFSI pilot-testing is one component of the Partnership Project on the Double Burden of Malnutrition, funded by the Canadian International Development Agency for 6 years (2008-2014). The Project assisted the government in the selection of pilot schools, fostered the installation of health and nutrition committees in selected schools, and helped with the initial school self-assessments. In accordance with the empowering philosophy of health promotion, pilot schools did not follow a pre-defined schedule of interventions, except for the training of teachers in nutrition education and the nutritional (anthropometric) surveillance of schoolchildren. For the latter activities, technical assistance and seminal funds were provided. Yearly planning workshops were held for school committees, with WHO support. In both settings, training was given to street vendors in order to improve the hygiene and nutritional value of food sold to schoolchildren. Other activities included special nutrition events and sanitation measures. In both cities, NFSI showed promising results in terms of school and community mobilization towards improved nutrition and health; however, NFSI must be better understood as an endogenous and self-sustaining approach. Furthermore, household poverty and scarce school resources appear as major barriers to gaining full impact of NFSI in low-income populations.