We have investigated glucose-6-phosphate dehydrogenase (G6PD) deficiency in 220 unrelated aboriginal male subjects who belong to three different tribes (Saisiat, Ami, and Yami) in Taiwan. Our results show that the G6PD deficiency rates for Saisiat, Ami, and Yami people are 9.0% (6/67), 6.1% (6/99), and 0% (0/54), respectively. Among these deficiency cases, 4 of 6 (66.7%) Saisiat subjects have the 493 A-->G mutation and one carries the 1376 G-->T mutation, whereas, in Ami subjects, we found that four of six (66.7%) affected males have the 592 C-->T mutation and one carries the 493 A-->G mutation. These results contrast with our previous findings for Taiwan Chinese, in whom the 1376 G-->T mutation is the major mutant allele and accounts for 52.3% of the deficiency cases. This is the first report of G6PD deficiency characterized at the DNA level in Taiwan aboriginal populations.