Background: Multiple factors determine children's nutritional status, including energy and nutrient intake, recurrent infectious diseases, access (or lack thereof) to clean water and improved sanitation, and hygiene practices, among others. The "Vegetables go to School: improving nutrition through agricultural diversification" (VgtS) project implements an integrated school garden programme in five countries, including Burkina Faso. The aim of this study was to determine the prevalence of undernutrition and its risk factors among schoolchildren in Burkina Faso before the start of the project. Methods: In February 2015, a cross-sectional survey was carried out among 455 randomly selected children, aged 8-14 years, in eight schools in the Plateau Central and Centre-Ouest regions of Burkina Faso. Nutritional status was determined by anthropometric assessment. Helminth and intestinal protozoa infections were assessed using the Kato-Katz and a formalin-ether concentration method. A urine filtration technique was used to identify Schistosoma haematobium eggs. Prevalence of anaemia was determined by measuring haemoglobin levels in finger-prick blood samples. Questionnaires were administered to children to determine their knowledge of nutrition and health and their related attitudes and practices (KAP). Questionnaires were also administered to the children's caregivers to identify basic household socio-demographic and economic characteristics, and water, sanitation and hygiene (WASH) conditions. To determine the factors associated with schoolchildren's nutritional status, mixed logistic regression models were used. Differences and associations were considered statistically significant if P-values were below 0.05. Results: Complete datasets were available for 385 children. The prevalence of undernutrition, stunting and thinness were 35.1%, 29.4% and 11.2%, respectively. The multivariable analysis revealed that undernutrition was associated with older age (i.e. 12-14 years compared to <12 years; adjusted odds ratio (aOR) = 3.45, 95% confidence interval (CI) 2.12-5.62, P < 0.001), multiple pathogenic parasitic infections (aOR = 1.87, 95% CI 1.02-3.43, P = 0.044) and with moderate and severe anaemia in children (aOR = 2.52, 95% CI 1.25-5.08, P = 0.010). Conclusions: We found high prevalence of undernutrition among the children surveyed in the two study regions of Burkina Faso. We further observed that undernutrition, anaemia and parasitic infections were strongly associated. In view of these findings, concerted efforts are needed to address undernutrition and associated risk factors among school-aged children. As part of the VgtS project, WASH, health education and nutritional interventions will be implemented with the goal to improve children's health.