Analysis of amino acids in blood or urine is a valuable diagnostic tool in cases of suspected metabolic disorders. The presence of a characteristic pattern of elevated amino acids is very useful in the diagnosis of these rare disorders. The detection of an apparently normal pattern of amino acids is also helpful to the clinician since it will eliminate many inborn errors of metabolism from the list of potential disorders. Methodologies for amino acid analysis in physiological fluids range from the very simple thin layer chromatography to automated low pressure or high pressure chromatography. Low pressure chromatography using a Beckman analyzer or similar instrument is the most common methodology for physiological amino acid analysis. Chromatography (HPLC) systems for amino acid analysis of proteins are available that can be modified for use with physiological samples. Waters makes a system called Picotag(TM) and Applied Biosystems makes an automated analyzer. These HPLC systems have some advantages over LPLC systems, including lower equipment cost, less caustic buffer systems and improved separation of certain amino acids.