Haplotype analysis of the phenylalanine hydroxylase (PAH) gene was performed on 27 chromosomes from a sample of 14 Greek phenylketonuria (PKU) probands and their parents. The majority (94%) of the 17 mutant PAH alleles are on haplotypes 1, 2 and 4, with haplotype 1 being most common. Sixty per cent of ten control PAH alleles are on haplotypes 1, 2 and 4. Haplotype 3 was not present in either group. A new MspI restriction site was found in exon 9 of a single mutant PAH allele on haplotype 7. The mutation responsible for the restriction site alteration is a T to C transition at nucleotide 1154 of the PAH cDNA, resulting in the conversion of codon 311 from leucine to proline (L311P). The same mutation has been described on a haplotype 1 allele in a German PKU patient. A single crossover event would be required to transfer this mutation from haplotype 1 to 7. Migration of this mutation from one haplotype to another by recombination cannot be distinguished from a recurrent mutation at this site.