Abstract Body: The waist-to-height ratio (WHtR) is a valuable tool for assessing central obesity and cardiometabolic risk, even in non-obese individuals. Childhood obesity is linked to metabolic abnormalities underlying cardiovascular diseases. Amino acids are fundamental in several metabolic processes, such as synthesizing proteins, ATP, and neurotransmitters. Organic acids are products of the metabolism of amino acids, carbohydrates, and fats. We assessed the hypothesis that their levels can serve as biomarkers for exposure, disease progression, and susceptibility, aiding in early intervention strategies. This cross-sectional study assessed amino acids and organic acids profiles in urine from prepubescent children categorized by WHtR. The 110 Brazilian participants aged 9-10 were classified as higher (n=48) or normal (n=62) cardiovascular risk. LC-MS/MS analyzed 47 amino acids and 73 organic acids in 12-hour urine samples, concentration values were adjusted by urinary creatinine. Standard protocols were used to obtain biochemical profiles, cardiovascular and anthropometric parameters. A metabolic signature in the urine of prepubescents at higher cardiometabolic risk was characterized by increased levels of the aromatic amino acids [Tyr (131 vs 90, p < 0.01), Trp (109 vs 95, p =0.02) and Phe (65 vs 46, p = 0.04)], Lys (212 vs 160, p < 0.01), α-aminoadipic acid (61 vs 49, p < 0.01), and cystathionine (25 vs 21 nmol/mg of creatinine, p = 0.03) while the levels of the organic acids p-OH-phenyl lactic (4.82 vs 3.7 ug/mg of creatinine, p = 0.02), suberylglycine (0.37 vs 0.18, p = 0.01), and benzoic acid (2.67 vs 1.77, p = 0.01) were found to be reduced. These amino acids were correlated with increased anthropometric measurements, low HDL-C, and hypertriglyceridemia. Also, Lys and Tyr were positively associated with higher systolic blood pressure. The organic acids were negatively correlated with anthropometric measurements and benzoic acid showed a positive correlation with time of exclusive breastfeeding. Findings indicate that children at higher cardiometabolic risk present an amino acid and organic acid signature in urine, this amino acid signature is commonly reported in type 2 diabetes and adults with cardiovascular disease. The organic acid signature in the urine of children in the context of cardiometabolic risk is reported for the first time.