Background: Despite ACADS (aryl-CoA dehydrogenase, short-chain) gene susceptibility variants (c.511C \textgreater T and c.625G \textgreater A) are considered to be non-pathogenic, encoded proteins are known to exhibit altered kinetics. Whether or not, they might affect overall fatty acid beta-oxidation still remains, however, unclear. Methods: De novo biosynthesis of acylcarnitines by whole blood samples incubated with deuterated palmitate (16-H-2(3),15-H-2(2)-palmitate) is suitable as a fluxomic exploration to distinguish between normal and disrupted beta-oxidation, abnormal profiles and ratios of acylcarnitines with different chain-lengths being indicative of the site for enzymatic blockade. Determinations in 301 control subjects of ratios between deuterated butyrylcarnitine and sum of deuterated C2 to C14 acylcarnitines served here as reference values to state specifically functional SCAD impairment in patients addressed for clinical and/or biological suspicion of a beta-oxidation disorder. Results: Functional SCAD impairment was found in 39 patients. The 27 patients accepting subsequent gene studies were all positive for ACADS mutations. Twenty-six of 27 patients were positive for c.625G \textgreater A variant. Twenty-three of 27 patients harbored susceptibility variants as sole ACADS alterations (18 homozygous and 3 heterozygous for c.625G \textgreater A, 2 compound heterozygous for c.625G \textgreater A/c.511C \textgreater T). Conclusion: Our present fluxomic assessment of SCAD suggests a link between ACADS susceptibility variants and abnormal beta-oxidation consistent with known altered kinetics of these variants.