In order to characterize the molecular heterogeneity of phenylalanine hydroxylase deficiencies in the Spanish population, 37 PKU patients were initially screened for 16 known European mutations. For the remaining unidentified alleles, we used a combined strategy based on single strand conformation polymorphism analysis and DNA sequencing. Overall, a total of 15 different mutations were found in our sample, which account for 62% of the total mutant alleles. We also investigated the association between the mutations, haplotypes and variable number of tandem repeats described on the phenylalanine hydroxylase gene. In addition, we analyzed the geographical distribution in Spain of the two most prevalent mutations in our population: IVS10 and I65T.