Background. Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency leads to impaired cortisol biosynthesis. Treatment includes glucocorticoid supplementation. We studied the specific metabolomics signatures in CAH patients using two different algorithms. Methods. In a case-control study of CAH patients matched on sex and age with healthy control subjects, two metabolomic analyses were performed: one using MetaboDiff, a validated differential metabolomic analysis tool and the other, using Predomics, a novel machine-learning algorithm. Results. 168 participants were included (84 CAH patients). There was no correlation between plasma cortisol levels during glucocorticoid supplementation and metabolites in CAH patients. Indoleamine 2,3-dioxygenase enzyme activity was correlated with ACTH (rho coefficient = −0.25, p-value = 0.02), in CAH patients but not in controls subjects. Overall, 33 metabolites were significantly altered in CAH patients. Main changes came from: purine and pyrimidine metabolites, branched aminoacids, tricarboxylic acid cycle metabolites and associated pathways (urea, glucose, pentose phosphates). MetaboDiff identified 2 modules that were significantly different between both groups: aminosugar metabolism and purine metabolism. Predomics found several interpretable models which accurately discriminated the two groups (accuracy of 0.86 and AUROC of 0.9). Conclusion. CAH patients and healthy control subjects exhibit significant differences in plasma metabolomes, which may be explained by glucocorticoid supplementation. Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive diseases due to enzyme deficiencies leading to impaired cortisol biosynthesis and deficiency of the 21-hydroxylase enzyme is its most common form. Main treatment relies on steroid replacement therapy including glucocorticoids (GC) (i.e. hydrocortisone) alone or in association with mineralocorticoids (i.e. fludrocortisone) 1. Although effective, long-term GC replacement therapy is associated with multiple adverse effects. They include, but are not limited to the appearance of cardiovascular metabolic risk factors (hypertension, insulin-resistance, obesity and dyslipidemia), immunosuppression with infections, psychological disturbances and osteoporosis. Moreover, oral GC intake does not supplement adequately cortisol's physiological circadian rhythm, and the dosage needed to suppress androgens is usually higher than that needed for substitution only 2. These elements all contribute to increased health costs and decrease of quality of life and life expectancy 2-6 .