Acylcarnitines in urine from 45 patients with organic acidemias and fatty acid oxidation disorders were evaluated using ESI-MS/MS. The urinary acylcarnitine profiles in organic acidemias, SCAD deficiency and MCAD deficiency were compatible with blood acylcarnitine profiles, and abnormalities in urinary acylcarnitine profiles in these conditions were enhanced following carnitine loading. Urinary acylcarnitine profiles were not helpful for characterization of long-chain fatty acid disorders, but a combination of urine and blood acylcarnitine analysis was useful for differential diagnosis of carnitine deficit.