Malnutrition is widespread among rural and nomad populations in the Sahel. It is linked to socio-economic factors and exhibits significant seasonal variations. The aim of this study was to assess the prevalence of malnutrition and associated risk factors among children less than 5 years of age. A repeated cross-sectional study design based on interviews and anthropometric measurements was used. A total of 653 nomad children and 579 sedentary children ranging in age from 0 to 59 months were randomly selected in households/camps on the south-eastern shore of Lake Chad. Data were collected from the same number of children at the end of the dry season (May/June, 2007) and at the end of rainy season (October 2007). Findings showed significant interseasonal variation in the prevalence of global acute malnutrition (GAM) between the end of the dry season and end of the rainy season. The respective variations were 17.9% to 13.7% (p = 0.03) in nomad children and 16.5% to 10.6% (p = 0.004) in sedentary children. Backward stepwise multivariate analysis by logistic regression showed that GAM among children under 5 years of age was significantly correlated with the following risk factors: seasonal variation, child's age, mother's nutritional status, ethnic group, and place of residence (LRT=172 and p < 0.001 for the logistic regression model). These findings demonstrate the critical state of the nutritional situation in the Sahel and rural areas.