A total of 1,342 blood samples from five aboriginal groups in Taiwan, comprising 522 of the Ami, 246 of the Bunum, 227 of the Atayal, 214 of the Paiwan and 133 of the Yami group, were collected. A complete blood count was performed in each case. In subjects with a mean corpuscular volume < 85 fl or hemoglobin (Hb) < 12 gm% (female) or 13 gm% (male), quantitation of Hb A2 and DNA analysis of alpha- and beta-globin genes were performed. Alpha-thalassemia was diagnosed by Southern hybridization of subject's DNA to alpha-, and zeta-globin gene fragments, and to Lo probe if needed. DNA from beta-thalassemia carriers was studied by polymerase chain reaction and direct sequencing. In the Ami, 42 (8.2%) were alpha-thalassemia 1 carriers, 42 (8.2%) were alpha-thalassemia 2 carriers, one had Hb H disease, and four (0.8%) were beta-thalassemia carriers. In the Bunun, one (0.2%) was an alpha-thalassemia 1 carrier, and two (0.4%) were alpha-thalassemia 2 carriers. In the Atayal, one (0.2%) was an alpha-thalassemia 1 carrier. In the Paiwan, seven (3.3%) were alpha-thalassemia 1 carriers, and one (0.5%) was an alpha-thalassemia 2 carrier. In the Yami, none were either alpha- or beta-thalassemia carriers. Diverse genetic origin, intragroup breeding and malarial selection may play a role in the significant differences of thalassemia prevalences both between the Chinese and the aborigines, and among different groups of aborigines.