Three rare beta-thalassemia mutations, not reported previously in Asian Indians or the Pakistani population, were identified by single strand conformation polymorphism analysis followed by direct sequencing. Two mutations, IVS-II-848 (C-->A) and initiation codon (ATG-->ACG), were found in the homozygous condition in patients belonging to Balochi and Sindhi ethnic groups of Pakistan, together with heterozygous and homozygous alpha(-3.7) deletions, respectively. A frameshift mutation at codon 44 (-C) was identified in a patient belonging to the Gujrati ethnic group together with IVS-I-1 (G-->T) and a normal complement of four a-globin genes. Haplotype analysis was performed to identify the chromosomal background associated with these mutations, and for tracing the origin and spread of these mutations.