Using amplification, allele-specific oligonucleotide (ASO) hybridization and DNA sequencing we have documented the molecular basis of 64 alpha- and 123 beta-thalassemia (thal) chromosomes, and the haplotypes of 18 beta S chromosomes from patients followed in three hospitals in Kuwait. Of the 30 chromosomes from 15 patients with Hb H disease, 26 (86.7%) carried the polyadenylation (poly A) signal mutation (AATAAA-->AATAAG) in the alpha 2-globin gene, 3 (10%) had the -alpha (3.7 kb) deletion, and 1 (3.3%) had the pentanucleotide deletion in the 5' IVS-I splice junction (alpha-5nt alpha). As many as 12 different beta-thal mutations were identified; 6 Mediterranean alleles [IVS-II-1 (G-->A), IVS-I-6 (T-->C), codon (CD) 39 (C-->T), IVS-I-110 (G-->A), CD 8 (-AA), and IVS-I-1 (G-->A)] were present in 79 (64.2%) of the chromosomes tested. Four East Indian alleles [IVS-I-5 (G-->C), IVS-I 3' end -25 nt deletion, CDs 8/9 (+G), and 619-bp deletion] were found in 31 (25%), and the two Kurdish/Iranian alleles [CD 44 (-C) and CDs 36/37 (-T)] were found in 13 (10.6%) chromosomes. Fourteen beta S chromosomes carried haplotype No. 31 (Saudi Arabia/India); 3 had haplotype No. 19 (Benin), and 1 was a hybrid with haplotype No. 31-specific characteristics in the locus control region hypersensitive site-2 (LCR-HS-2), and haplotype No. 19-specific mutations in the 5' flanking region of the G gamma-promoter. The patient homozygous for haplotype No. 19 was a Jordanian, while the others were Kuwaiti Arabs. The latter appear to be fairly homogeneous in terms of the prevalent alpha-thal determinants and beta S-haplotypes, but there is considerable heterogeneity of their beta-thal alleles. This has implications for genetic counseling and prenatal diagnosis programs.