We describe a mutation analysis for the phenylalanine hydroxylase gene and the clinical outcome of two Japanese patients with non-phenylketonuria (PKU) hyperphenylalaninemia (serum phenylalanine level below 600 mumol/l under a free diet) detected by a mass-screening program. Single strand conformation polynorphism analysis and direct sequencing of their genomic DNAs revealed that non-PKU hyperphenylalaninemia resulted from compound heterozygosity for a mutation causing classical PKU and a mutation with a milder effect on phenylalanine hydroxylase activity. The mutations were R241C and R243Q in exon 7, and R413P in exon 12. The mutation genotypes of the two patients were R241C/R243Q and R241C/R413P. It has been demonstrated that homozygosity for the R243Q or R413P mutation is associated with a severe phenotype of PKU and low in vitro expression activity. In contrast, the R241C mutation has much less effect on phenylalanine hydroxylase activity. The metabolic consequence of each variant allele was confirmed by a phenylalanine loading test in the patients and their parents. The patients achieved normal results in all intellectual and neurologic tests. Brain magnetic resonance imaging revealed no abnormalities. The dietary restriction was continued until 10 years of age in order to maintain the serum phenylalanine level below 400 mumol/l. The genetic analysis to distinguish non-PKU hyper-phenylalaninemia from classical PKU helps to determine the principles of dietary management in the early infantile period.