BACKGROUND: Trends in the nutritional status for developing countries that are undergoing rapid economic growth indicate a decrease in protein-energy malnutrition (PEM) with an associated rise in obesity prevalence. OBJECTIVE: This paper analyses how supplementary feeding programmes may contribute to rising obesity trends, what factors may explain this phenomenon, and potential strategies to avoid obesity in malnutrition prevention efforts. DESIGN AND SETTING: This is a descriptive study of changes in nutritional status of infants and young children in Chile and the possible impact of supplementary feeding programmes on the rise in prevalence of obesity. We explored the changes in anthropometric indices before and after receiving food programme benefits and the use of targeting strategies as a way to combine the need to promote optimal growth while preventing obesity. RESULTS: Evaluation of the change in nutritional status from participants in Chilean supplementary feeding programmes has shown that targeting strategies have been inadequate as children mainly modify their weight-for-age and weight-for-height, while their length-for-age remains practically unchanged. CONCLUSIONS: Monitoring length-for-age as well as weight-for-length is necessary to permit the identification of stunted overweight and obese children, as they should not be given excess energy. Energy supplementation should be adjusted according to activity level, securing adequate micronutrient density. PEM prevention programmes need periodic evaluation, including targeting of beneficiaries, definition of real needs and possible effect on obesity.