Acylcarnitines in amniotic fluid samples were analyzed for the prenatal diagnosis of propionic acidemia, methylmalonic aciduria, isovaleric acidemia, and glutaric aciduria by electrospray tandem mass spectrometry. Although the levels of the specific acylcarnitine between affected and unaffected cases showed an overlap, the ratios of propionylcarnitine to 4-carbon acylcarnitine levels for propionic acidemia and methylmalonic aciduria, those of isovalerylcarnitine to propionylcarnitine for isovaleric acidemia, and those of glutarylcarnitine to propionylcarnitine for glutaric aciduria type I were shown to be reliable indicators in the prenatal diagnosis. In addition, it is suggested that the combination of the ratios of glutarylcarnitine, isovaleryl-carnitine, and hexanoylcarnitine to propionylcarnitine may be useful for the prenatal diagnosis of glutaric aciduria type II.