The Southeast Asia type deletion of alpha-thalassemia-1 (--SEA) is the most common type of alpha-thalassemia-1 in Taiwan. There are 2 less common types, Filipino type (--FIL) and Thai type (--THAI). In the current study, we screened 754 cases of alpha-thalassemia-1 in Southern Taiwan using a polymerase chain reaction (PCR)-based method. Our results show that the prevalence of the (--SEA) type is 90.6%, followed by the (--FIL) type (8.6%), the (--THAI) type (0.5%), and the (-alpha(3.7/-alpha(3.7)) type (0.3%). We also analyzed the genotypes of 96 patients with hemoglobin (Hb) H disease and 48 cases of hydrops fetalis with Hb Bart's. The frequencies of the genotypes of the alpha-thalassemia-1 allele in Hb H disease are in accordance with the results of analyses of alpha-thalassemia-1 cases. The alpha-thalassemia-2 allele includes alpha(4.2), alpha(G), alpha(CS), and alpha(QS)alpha. Forty-one cases, 6 cases, and 1 case of hydrops fetalis with Hb Bart's were caused by --SEA/--SEA, --SEA/--FIL and --SEA/--THAI respectively. The genotypes and frequencies of alpha-thalassemia in this study are different from those in previous studies in Taiwan and Hong Kong. These differences may be attributed to the diverse genetic origin among different ethnic groups and the extensive inclusion of the (--FIL) and (--THAI) alpha-thalassemia-1 types.