Mass spectrometry is an important part of multicomponent analytical systems designed for diagnosis of metabolic disorders. In our laboratory capillary gas chromatography/mass spectrometry (GC/MS) with computerized library search is used primarily to separate and identify urinary organic acids. About 50 different diseases with increased excretion of organic acids are recognized today. Other techniques, including thin-layer chromatography, high-performance liquid chromatography with diode array detector, automatic amino acid analysis and two-dimensional electrophoresis are used to detect other compounds of diagnostic significance. The diagnostic use of GC/MS is exemplified by studies on two siblings. One died of his disease at approximately 1 year old. Both excreted 3-hydroxydicarboxylic acids (C8-C12) as identified by mass spectrometry. These metabolites are secondary to systemic carnitine deficiency. Low-fat diet normalized the clinical condition of the surviving sibling. GC/MS is now used to monitor the efficacy of dietary treatment by analysing the dicarboxylic acid excretion in this patient. Modern DNA technology is rapidly becoming increasingly important for diagnosis, particularly prenatal diagnosis, of metabolic diseases. It is suggested, however, that mass spectrometry will continue to be an important diagnostic tool for many years ahead.