We have developed a rapid method to molecularly distinguish different types of Hb H disease. The study depended on (a) most of the Hb H disease in Taiwan having an alpha-thalassemia-1 of the Southeast Asia type (-SEA) in one allele and (b) the differences of X box of alpha-globin gene cluster in the other allele. To detect the -SEA allele, we utilized the primers located on either side of the breakpoint to do PCR, then characterized the amplified products. For the other allele, we sequenced part of the X box, and found that bases -2803 to -2461 of the X box of - alpha(3.7), belonged to the X box of alpha(2) globin gene. In - alpha(4.2), the bases belonged to the X box of alpha(1) globin gene, whereas in alpha(cs)alpha it contained both X boxes of alpha(1) and alpha(2) globin genes. There was an MboII site at this region of the X box of a, globin gene. We utilized PCR to amplify this region and digested it with restriction enzyme MboII, then combined it with another PCR of different primer pairs to molecularly diagnose different types of Hb H disease. One hundred and one cases of Hb H disease from different families were studied: all of the cases had one allele of -SEA deletion, while the other allele showed that 52/101 were -alpha(3.7), 41/101 were alpha(cs)alpha, 71/101 were -alpha(4.2), and 1/101 was -alpha(G.Taichung). Of 52 cases of Hb H with -alpha(3.7), 47 were type-I deletion and five were type II deletion.