In recent years, tandem mass spectrometry has generated great interest as a method for neonatal screening. The basic principle is electronically controlled separation of analytes by their mass-to-charge ratio. The advantage of this detection system is speed, the capability to analyze for many different compounds in a single analysis, and a minimal need for auxilliary assay reagents. The prevailing screening technique uses stable isotope dilution, butylesterification, and MS/MS analysis to quantify amino acids and acylcamitines in neonatal dried blood spot samples. This allows detection of more than 30 inborn errors of metabolism of amino acids, fatty acids, and other organic acids. In Denmark, a large-scale pilot study is being implemented to evaluate the screening potential of tandem mass spectrometry. National patient registers and medical records from clinical genetics units are used to identify cohorts of healthy infants and infants with selected inborn errors of metabolism. The neonatal screening samples of these infants are retrieved from a biobank and are assayed for amino acids and acylcarnitines using tandem mass spectrometry. This study yields decision values for neonatal screening, which will be evaluated in a subsequent 2-year prospective pilot study, offering the test to 140,000 neonates as a voluntary adjunct to the existing screening program. The organization consists of integrated units for neonatal screening and clinical genetics. The effect of the program will be assessed in terms of screening efficiency, cost and short term clinical outcome.