Although the average frequency of beta-thalassaemia carriers in India is 3-4% and the prevalent mutations have been studied, no micromapping has been done. This is the first attempt to provide an accurate estimate of the frequencies of beta-thalassaemia and the expected annual births of homozygous children in different districts of Maharashtra and Gujarat in Western India as well as to determine the molecular heterogeneity in different sub-regions in these states. A total of 18 651 individuals were screened for haemo-globinopathies and mutations were characterized in 1334 beta-thalassaemia heterozygotes. There was an uneven distribution of the frequencies of beta-thalassaemia, varying from 1.0% to 6.0% and 0% to 9.5% in different districts of Maharasthra and Gujarat. The rate of homozygosity per 1000 births annually was 0.28 in Maharashtra and 0.39 in Gujarat. The three most prevalent beta-thalassaemia mutations in Maharashtra were IVS 1-5(G-->C), Codon 15(G-->A) and Codon 30(G-->C) (87.9%) while in Gujarat they were IVS 1-5(G-->C), 619 bp deletion and Codon 5(-CT) (68.5%). These data will help to develop adequate programmes for control and care where they are most needed. They also emphasize the importance of subgroup micromapping for determining the health burden of a common genetic disease.