Examining individual life-histories provide a direct way to understand the mechanisms of population's adaptation to major ecological and socio-cultural changes. The Mesolithic- Neolithic transformations offer a convenient frame to develop this bottom-up approach. The Neolithic transition, the passage from mobile foraging to sedentary farming, was a major shift during human prehistory. Focusing on the Balkan region where Early Neolithic started around 6200 cal BC, this paper presents stable isotope results (carbon, nitrogen, sulfur) of an intra-individual sampling strategy (data on bone and deciduous/permanent teeth) performed on 30 children from Mesolithic and Neolithic sites situated across Serbia and Croatia. Results suggest significant differences in the feeding practices of Mesolithic and Neolithic children as well as regional differences in mother's dietary choices. This study opens new horizons on the relationship between individuals subsistence strategies and the dynamic of the group, implying that these bio-cultural differences may contribute to the important demographic changes observed at the Mesolithic-Neolithic transition.