Thalassaemia is the most common inherited disorder in Pakistan and there are very inadequate treatment facilities for over 4000 homozygotes born each year. Prevention of these disorders therefore forms an essential part of the management of this enormous health problem. We have characterized 1216 beta-thalassaemia alleles from the five major ethnic groups of Pakistan. The complete spectrum comprised 19 different mutations. There are important ethnic and regional differences in the prevalence of mutations. The five most common mutations, IVSI-5 (G-C) (37.3%), Fr 8-9 (+G) (25.9%), del 619 (7.0%), Fr 41-42 (-TTCT) (6.7%) and IVSI-1 (G-T) (5.4%), constitute 82.3% of the total. Fr 8-9 (+G) is the most common mutation in Northern Pakistan (41.3%), whereas IVSI-5 (G-C) is the most frequent mutation in Southern Pakistan (52.2%). Six subjects with transfusion-dependent thalassaemia major showed only a single mutant allele. One subject with transfusion-dependent thalassaemia major showed a novel 17 bp deletion involving Cd126-131. Our findings provide a comprehensive basis for carrying out prenatal diagnosis of thalassaemia in a geographical area where it is found in high frequency.