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The Nutrition-Friendly School Initiative was developed in 2006 to counter the double burden of malnutrition and implemented on a pilot basis in primary schools in Ouagadougou (Burkina Faso) in 2009. A baseline study was conducted in intervention and control schools and repeated in 2014 to assess the impact. This paper reports on anthropometric and biochemical data in the final and baseline surveys. Both studies were conducted in the fifth grade classes of the same primary schools in Ouagadougou. Six intervention schools had been selected and matched at baseline with six control schools. The total sample consisted of 699 and 651 pupils in 2009 and 2014, respectively. Anthropometric and hemoglobin measurements were performed on all children, whereas serum retinol was measured in a random subsample to assess Vitamin A Deficiency (VAD). Independent t -tests and chi-squared tests were used for comparison of means and proportions, respectively, and multiple logistic regressions were conducted to examine associations between nutritional parameters and school characteristics. Final rates of anaemia and VAD were 32.6% and 26.1%, respectively, down from 40.4% and 38.7% at baseline. The final prevalence rate of stunting was 8.1%, thinness was 8.7% and overweight/obesity was 4.4%. Thinness declined significantly in 2014 compared to 2009, but there was no change in the rate of stunting even though the rate of overweight/obesity showed an upward trend. When comparing intervention with control schoolchildren, the only significant differences found in the final survey were less thinness and less anaemia in the intervention children. However, the prevalence of anaemia was also significantly lower in the intervention group at baseline. Our results point to a significant improvement in the nutritional status of schoolchildren in Ouagadougou and suggest a positive, although modest, role for the Nutrition-Friendly School Initiative in reducing thinness, but not overweight.