Direct analysis of unpurified urine from patients with beta-ketothiolase deficiency and glutaryl-coenzyme A dehydrogenase deficiency was carried out by methylation and fast atom bombardment mass spectrometry. Previously unidentified signals consistent with unusual acylcarnitines were detected. In the former disease, thermospray liquid chromatography/mass spectrometry analysis confirmed the identification of tiglylcarnitine and differentiated it from a biological isomer, 3-methylcrotonylcarnitine. In glutaric aciduria, glutarylcarnitine was confirmed by detection of glutaric acid liberated upon base hydrolysis of a purified acylcarnitine fraction. The discovery of these metabolites suggests that L-carnitine therapy might be beneficial for the enhanced excretion of toxic metabolites that accumulate in patients with these disorders.