Common alpha-thalassemia (thal) rearrangements were studied in a normal random population and in six ethnic groups of Pakistan. Analyses of 204 individuals from the normal population revealed the presence of only the -alpha(3.7) allele with an overall frequency of 8.3%. Ethnic differences were statistically significant for Pashtoon vs. Balochi (p < 0.0005) and Pashtoon vs. Sindhi (p < 0.002). Two hundred and eighty-five thalassemia patients were also studied to identify rare alpha-thal alleles. In this group, 24.6% of the patients had one or two alpha genes deleted. Two rare alleles in the Pakistani population, -alpha(4.2) (0.2%) and alphaalphaalpha(anti3.7) (0.9%), were identified in these patients. The -alpha(4.2) allele was found only in Sindhis, while alphaalphaalpha(anti3.7) was present in Punjabis, Sindhis and Balochis. Five patients with triplicated alpha genes were homozygous for either the beta+ or the beta(0) genotype.