Faster growth seems to be a common factor in several hypotheses relating early life exposures to subsequent health. This study aims to investigate the association between body mass index (BMI) trajectories during infancy/childhood and later metabolic risk in order to identify sensitive periods of growth affecting health. In a first step, BMI trajectories of 3301 European children that participated in the multi-centre Identification and Prevention of Dietary and Lifestyle-induced Health Effects in Children and Infants (IDEFICS) study were modelled using linear-spline mixed-effects models. The estimated random coefficients indicating initial subject-specific BMI and rates of change in BMI over time were used as exposure variables in a second step and related to a metabolic syndrome (MetS) score and its single components based on conditional regression models (mean age at outcome assessment: 8.5 years). All exposures under investigation, i.e. BMI at birth, rates of BMI change during infancy (0 to <9 months), early childhood (9 months to <6 years) and later childhood (≥6 years) as well as current BMI z-score were significantly associated with the later MetS score. Associations were strongest for the rate of BMI change in early childhood (1.78 [1.66; 1.90]; β estimate and 99 % confidence interval) and current BMI z-score (1.16 [0.96; 1.38]) and less pronounced for BMI at birth (0.62 [0.47; 0.78]). Results slightly differed with regard to the single metabolic factors. Starting from birth rapid BMI growth, especially in the time window of 9 months to <6 years, is significantly related to later metabolic risk in children. Much of the associations of early BMI growth may further be mediated through the effects on subsequent BMI growth.