We have performed a pilot study of neonatal mass screening for inborn errors of metabolism (IEM) by gas chromatography-mass spectrometry (GC/MS) using urine specimens in the Shimane area. In this project, 1,686 babies born in several institutes in Shimane were screened for 18months from May, 1996 to October, 1997. The automated metabolic profiling and disease detection system developed by us was applied to this screening. Patients with definite IEM were not identified, but several transient abnormalities in the neonatal period, such as elevation of 4-hydroxyphenyllactate, galactose, or 3-hydroxy-3-methylglutarate, were observed in 112 (6.2%), in particular, more frequently in low birth weight infants. In order to test the usefulness of our screening system, samples from 13 patients with 9 different metabolic disorders previously diagnosed were analyzed. Consequently, methylmalonic acidemia, isovaleric acidemia and glyceroluria were detectable without fail. In cases of propionic acidemia, phenylketonuria, maple syrup urine disease, ornitine transcarbamylase deficiency or glutaric aciduria type 2,the detection of their diagnostic marker metabolites seemed unstable.