Many genetic diseases, especially the inborn errors of metabolism, have very low incidences, so developing a newborn screening test for each disease is not practical. This obstacle was overcome by employing the tandem mass spectrometry (MS/MS) technology. In the analysis, the samples can be injected directly into the flowing system without passing through a column, and both acylcarnitine and amino acid profiles can be obtained at the same time. MS/MS newborn screening has been shown to improve the outcome of patients affected by a number of inborn errors of metabolism. Recently, MS/MS analytical methods were developed for second-tier tests of newborn screening; new substrates have also been developed to measure the activity of lysosomal enzymes so lysosomal storage diseases can be diagnosed by MS/MS method now.