The molecular basis of beta-thalassemia in Lebanon reflects the heterogeneity of the Lebanese population. Eighteen different mutations were identified among a total of 277 chromosomes. There is evidence of clustering of some mutations in particular geographic regions or among specific religious groups. Haplotype analysis, using seven restriction sites was performed on a total of 110 samples and 11 different haplotypes were identified. The five most common mutations were each found on two different haplotypes, and most linkages were as previously reported in other Mediterranean populations, with a few exceptions, also showing some clustering.