Childhood malnutrition remains a major challenge to public health in poor countries. Data on malnutrition determinants in African children are scarce. A cross-sectional survey was performed in eight villages of Burkina Faso in June 2009, including 460 children aged 6-31 months. Demographic, socioeconomic, parasitological, clinical and anthropometric characteristics were collected. The main outcome variable was weight-for-length (WFL) z-score (i.e. wasting). A multiple regression model identified village, age group, religion and the presence of younger siblings as significantly associated with wasting. Villages differed in their mean WFL z-score by up to one unit. Compared with younger children, the mean WFL z-score of children aged 24-35 months was 0.63 units higher than the WFL z-score in younger children. This study confirms the still unacceptable high level of malnutrition in young children of rural West Africa and supports the fact that childhood malnutrition is a complex phenomenon highly influenced by contextual variables.