INTRODUCTION: Adverse exposures in utero might cause adaptations of cardiovascular and metabolic organ development, predisposing individuals to an adverse cardio-metabolic risk profile from childhood onwards. We hypothesized that adaptations in metabolic pathways underlie these associations and examined associations of metabolite profiles at birth with childhood cardio-metabolic risk factors. METHODS: The study included 763 mother-child pairs participating in an ongoing population-based prospective cohort study with an overall low disease risk. Cord blood serum concentrations of amino acids (AAs), nonesterified fatty acids, phospholipids and carnitines (Carn) were obtained using a liquid chromatography coupled with tandem mass-spectrometry. We measured android/gynoid fat mass ratio, blood pressure, insulin, and lipid concentrations at the children's age of 5.9 (0.3) and 9.8 (0.9) years. RESULTS: We did not observe associations of cord blood metabolites with systolic or diastolic blood pressure, insulin, triglycerides, and android/gynoid fat mass ratio at both ages and cardio-metabolic risk clustering at age 10 years. Five short- and medium-chain Carn.a metabolites were positively associated with cardio-metabolic risk clustering at age 6 but did not survive more stringent confounder adjustment. CONCLUSION: No consistent associations between cord blood metabolites and cardiovascular risk factors at school age were observed.