This molecular genetics study was conducted in Karachi, Pakistan from 2004 to 2006 to provide guidelines for prenatal diagnosis programmes in the country. Blood samples of patients with beta-thalassaemia minor (n = 200) and beta-thalassaemia major (n = 150) were collected from hospitals, transfusion centres and diagnostic laboratories from different districts of Karachi, representing 5 major ethnic groups. Molecular analysis revealed 11 genetic mutations of the beta-thalassaemia gene, among which 5 mutations accounted for 88% of the total beta-thalassaemia genes identified [IVS-1-5 (G–C), Fr 8/9 (+G), Fr 41/42 (–TTCT), IVS-1-1 (G–T) and Del 619]. Other mutations identified were CAP+1, IVS-II-1 (G–A), Cd 5 (–CT), Cd 15 (G–A), Cd 16 and Cd 30.