In this study we have carried out haplotype analysis on the beta-globin gene cluster and characterized the beta-thalassemia mutation by oligonucleotide hybridization in 14 patients with thalassemia major and 5 with sickle cell/beta-thalassemia originating from southern Portugal. We found that three mutations, namely the beta(0)-39, beta(0) IVS-1 nt 1 and beta(+) IVS-1 nt 110 are prevalent accounting for 53%, 32% and 10% of the beta-thalassemia chromosomes respectively. In general each mutation was associated with a specific chromosomal haplotype; the beta(0)-39 mutation, however, was linked to three different haplotypes. These results indicate that three oligo-probes complementary to the most common mutations allow prenatal diagnosis by oligonucleotide analysis in 96% of the couples at risk of having offspring with thalassemia major in southern Portugal.