INTRODUCTION Hyperphenylalaninemias are inborn errors of phenylalanine metabolism caused by deficiency of L-phenylalanine hydroxylase (the enzyme that converts phenylalanine to tyrosine), resulting in increased serum phenylalanine (>4 mg/dL or 240 μmol/L). Phenylketonuria, or PKU, is the most common form. Untreated PKU is associated with progressive neurodevelopmental delay, evolving towards intellectual impairment. Cuba introduced a national newborn screening program for PKU in 1986. It has enabled early diagnosis and initiation of dietary treatment, reducing appearance of intellectual impairment in these patients. Originally, confirmatory diagnosis was done only by quantifying serum phenylalanine. In 2010, however, an HPLC method for quantifying serum phenylalanine and tyrosine simultaneously was validated at the National Medical Genetics Center, to perform confirmatory and differential diagnosis of hyperphenylalaninemias, as well as biochemical monitoring of patients diagnosed. OBJECTIVES Describe experience using HPLC confirmatory diagnosis for positive cases from the National Neonatal Screening Program for Phenylketonuria and in biochemical monitoring of diagnosed patients after initiation of dietary treatment. METHODS A descriptive retrospective case-series study was conducted from June 2010 through June 2012. The study population comprised 531 infants who tested positive in the National Neonatal Screening Program for Phenylketonuria. Variables used were serum phenylalanine concentration (first criterion of positivity) and tyrosine, phenylalanine/tyrosine ratio (second criterion, both detected by reverse-phase HPLC with direct fluorescence), hyperphenylalaninemia classification, year of diagnosis, sex, and province of origin. RESULTS Of the samples, 97.7% (519/531) were confirmed as false positives, and 10.4% (55/531) had transient neonatal tyrosinemia. Hyperphenylalaninemia was diagnosed in 12 infants (2.2%): 1.3% (7/531) presented classical PKU, with 34.7 ± 14.7 mg/dL phenylalanine in serum and phenylalanine/tyrosine ratio of 18.9 ± 12.7; and 0.9% (5/531) had persistent hyperphenylalaninemia, with 8.9 ± 3.4 mg/dL of phenylalanine and phenylalanine/tyrosine ratio of 4.5 ± 1.6. Matanzas Province contributed more cases than any of Cuba's 14 other provinces (3/12, 25%) and there was a slight predominance of male sex (7/12, 58.3%). During biochemical monitoring, 83.3% of patients (10/12) reduced their levels of phenylalanine (<5 mg/dL or 300 μmol/L): 5 with classical PKU and all 5 with persistent hyperphenylalaninemia. The incidence of neonatal hyperphenylalaninemias was 1/22,503 live births and 1/38,577 for classical PKU. CONCLUSIONS HPLC for simultaneous quantification of phenylalanine and tyrosine in serum meets the needs of a confirmatory test for patients testing positive in Cuba's National Neonatal Screening Program for Phenylketonuria (which has high false positive rates). It has enabled introduction in Cuba of a second PKU diagnostic criterion of positivity for both the classification of hyperphenylalaninemias and the biochemical monitoring of diagnosed patients.