Objective-To assess the benefits of using the phenylalanine:tyrosine ratio to screen newborns for phenylketonuria (PKU). Setting-Data were collected from all newborns in California during a ten month period (n = 404 381). Methods-Dried blood spot specimens were analysed at nine laboratories. To assure that the results reported from multiple sites were matched accurately, an automated methodology was chosen that included sample processing, analysis, telecommunications, reporting, and information technology. Phenylalanine and tyrosine concentrations were measured independently by continuous flow fluorometry, for which precision, recovery, detection limits, carryover, chemical specificity, reportable range, and number of repeats are reported. Results-In this study, 37% of the newborns were tested at less than 24 hours of age. For this population, using a phenylalanine only cut oV of 200 µmol/l, there were 48 recalled infants per case of classic PKU. Using the phenylalanine:tyrosine ratio with a cut oV of 1.50, screen positives could be reported with phenylalanine as low as 150 µmol/l and with only 12 recalls per case. Conclusions-The phenylalanine:tyrosine ratio can be measured accurately at multiple laboratories using two channel chemical analyses. Having applied the methods to the routine clinical screening of a large population, it was confirmed that the clinical sensitivity and specificity of the PKU screening test are higher when the phenylalanine:tyrosine ratio is incorporated into the cut oV than when the cut oV is based on the phenylalanine concentration alone. (J Med Screen 2000;7:131-135)