The rising worldwide prevalence of Metabolic Syndrome (MetS), a cluster of cardiometabolic risk factors predictive of type 2 diabetes, relates largely to increasing obesity and sedentary but also to early metabolic life events. The objective of the study was to develop accurate and robust markers of MetS as well as to bring new knowledge about this pathological state using a multidisciplinary approach. This casecontrol study (subjects free of MetS at baseline (n=92 born small vs n=76 born adequate for gestational age (SGA vs AGA)) was nested in the French community‐based Haguenau cohort. The control group was randomly matched for age and sex. Serum metabolic signatures were determined and compared at the end of follow‐up (30 years of age) to determine markers related to MetS using an untargeted mass spectrometry metabolomic approach. Statistical analyses allowed identifying 25 metabolites significantly modified according to the MetS phenotype in the whole population, and 42 among the SGA subjects, revealing a specific signature of the foetal imprinting. Correlation analyses with other data (anthropometric, clinical, and biochemical) contributed to better understand the role of these biomarkers in the pathological processes, and therefore to evaluate their potential clinical value.