Acylcarnitine profiling from blood or plasma samples by electrospray tandem mass spectrometry (ESI-MS/MS) has been recognized recently as a useful tool in the biochemical diagnosis of propionic acidemia, methylmalonic acidemia together with short-chain and medium-chain acyl-CoA dehydrogenase deficiencies. In the current study, we have investigated the diagnostic capabilities of ESI-MS/MS in other types of organic acidemias and amino acid catabolism disorders. Using multiple scanning functions, we examined the potential for the simultaneous profiling of both acylcarnitines and amino acids, in each of the samples. Our method was found to be specific and accurate; allowing quantification of acylcarnitines and amino acids well below, and significantly above, published normal levels. Complete automation of sample introduction has been achieved, allowing the analysis of up to 200 samples in one injection sequence, at a rate of one sample every 3 min, with excellent separation between successive injections. In our hands, this method permits screening for 20 organic acid and amino acid disorders, using a single sample injection. In our laboratory, more than 2000 blood samples have been analyzed, and 52 new cases were diagnosed by this method. We also confirmed the diagnosis of another 75 previously known cases.