The analysis of amino acids is the most frequently applied technique in the selective screening of inborn errors of metabolism. When urine is used as a starting material, simple techniques such as thin-layer chromatography or high-voltage electrophoresis is preferred as a first approach. The quantitative analysis requires instrumentation, usually an amino acid analyser. Both plasma and urine are needed for establishing renal transport defects. Apart from the accumulation of the 'usual' amino acids, the presence of unusual amino acids may be of diagnostic significance. Furthermore the finding of decreased plasma concentrations of specific amino acids may pinpoint several inherited defects. No amino acid screening procedure is complete without the availability of an organic acid and a purine/pyrimidine analytical system, both yielding important additional diagnostic information. Considerable clinical problems may occur in subjects with a decreased tolerance to protein amino acids without being homozygous for any inherited defect. Examples of these disorders that need further studies are homocysteinaemia associated with vascular disease and carriers of ornithine transcarbamylase deficiency.