Recognition of various phenylketonuria phenotypes has led to a variety of descriptive terms but classical phenylketonuria (PKU) may be defined as phenylalanine (PA) tolerance of 10-20 mg/kg/day at 5 years. The term 'mild PKU' indicates PA tolerance of 20-50 mg/kg/day whereas children with benign hyperphenylalaninaemia show normal development and are able to eliminate 100 mg/kg within 24 hours. The genetic basis for PKU has been investigated by reverse transcription via mRNA of the genes for phenylalanine hydroxylase (PH) present on chromosome 12q 22-24.1. The resulting complementary DNA sequence has been studied and the normal genes characterized. Following digestion of DNA from PKU patients and their families with restriction endonucleases, haplotype analysis has allowed identification of 12 restriction fragment length polymorphism haplotypes associated with normal and mutant PH alleles. Four haplotypes accounted for 91% of all mutant alleles in the Danish population studied. For heterozygotic parents it is possible to determine the haplotype associated with the normal allele and the mutant allele. Correlation between the different haplotypes and PKU phenotypes has allowed identification of the mutation responsible for classical PKU. Fifty eight per cent of mutant PKU alleles in the Danish population were found to be associated with 2 haplotypes and this is consistent with a founder effect in which the spread of mutant alleles passively follows the spread of these haplotypes in the European population. The phenotypical diversity of PH deficiency arises from multiple mutant alleles. Two mutations account for the majority of classical PKU in Denmark and since 75% of the Danish PKU population are heterozygotes for PH haplotypes, the various phenotypes reflect the composite activity and interactions of gene products from two mutant alleles.