We performed a cost-effectiveness analysis to evaluate whether a pediatrician who suspects an inherited disease of amino acid metabolism should refer the child to a specialist in inborn errors of amino acid metabolism or should prescribe the usual screening test, chromatography of amino acids. Actual hospital costs were used to value the referral, the tests, and the complications that occur when the diagnosis is not recognized. The percent of confirmed diagnoses was chosen as a measure of effectiveness. We conclude that it is more cost-effective for a pediatrician to refer the child to a specialist, that the best strategy in the absence of a referral is to prescribe thin-layer chromatography, and that the least cost-effective strategy is to perform ion-exchange chromatography immediately.