The clinical presentation of HbE-β-thalassemia is extremely variable, however, many cases are severe and transfusion dependent. We offered prenatal diagnosis to 108 couples, 20 of whom came prospectively. CVS was done in 93 cases (9.5-13 weeks of gestation) while amniocentesis/cordocentesis was done for 15 cases in the second trimester. Diagnosis was done by reverse dot blot hybridization, ARMS, DNA sequencing and in a few cases by HPLC analysis of fetal blood. The genetic combinations in the couples at-risk were the following: HbE trait/β-thal trait-95, HbE-thal/HbE trait-5, HbE homozygous/β-thal trait-3, HbE-thal/β-thal trait-3, HbE Lepore/β-thal trait-1, HbE trait/HbD trait-1. IVS1-5(G>C) was the commonest β-thalassemia mutation followed by codon15(G>A), codon30(G>C), codons41/42(-CTTT), the 619 bp deletion and codon8/9(+G) in the β-thalassemic parent. However, several rare mutations seen in India like -90(C>T), -88(C>T),codon15(-T), IVS1-129(A>C), IVS1-130(G>C), IVSII-1(G>A), IVSII-837(C>T) and IVSII 848(C>A) were also encountered. Twenty-one fetuses were affected (HbE-β-thal-20, β-thal major-1) and all the couples opted for termination of the pregnancies. Couples with affected children wish to undergo prenatal testing for HbE-β-thal in subsequent pregnancies. More regional centers are needed for these services, particularly in West Bengal and the North-East where HbE is very common.