There is a large variation of clinical severity among thalassemic patients in Sicily. A heterogeneous molecular basis has already been demonstrated among the patients presenting with thalassemia intermedia. The same approach, based mostly on linked haplotypes of the beta gene cluster polymorphisms and in some cases on the demonstration of the molecular defect itself, was used to investigate 55 patients presenting with severe Cooley anemia, all maintained under permanent transfusion regimen. A large heterogeneity was demonstrated in the observed haplotypes, and only a limited overlap with those already found in thalassemia intermedia. It has been noted that many of the patients are compound heterozygotes, the various observed associations making the antenatal diagnosis at the DNA level difficult in the near future.