Prompted by the fact that the urinary excretion of organic acids in the riboflavin-deficient rat closely mimics that found in patients with inborn errors in the acyl-CoA dehydrogenation systems, the organelle localization and the apparent kinetic constants (Km and Vmax values) for the rat liver acyl-CoA:glycine-N-acyltransferase (glycine-N-acylase) toward isobutyryl-CoA, 2-methylbutyryl-CoA, isovaleryl-CoA, butyryl-CoA, hexanoyl-CoA, octanoyl-CoA, decanoyl-CoA, and benzoyl-CoA were determined. The studies on organelle localization demonstrated that the glycine-N-acylase is exclusively an intramitochondrial enzyme, and that no activity is present in peroxisomes, which also possess ability to produce Acyl-CoAs. The kinetic studies were done in order to elucidate whether the quantitative differences in excretion profile of acylglycines between riboflavin-deficient rats and patients with beta-oxidation defects are caused by differences in ability to conjugate the various acyl-CoAs. It was found that the Km values for the rat liver enzyme were generally somewhat lower than the values found in man, but with the same chain length profile. Consequently, the above-mentioned differences in excretion profile of acylglycines between riboflavin-deficient rats and patients with beta-oxidation defects cannot be explained by differences in affinity toward the glycine-N-acylase.