There is a high prevalence of thalassemia in the Taiwan area. Prenatal diagnosis of severe forms of thalassemia is important for the prevention of this disease. We performed prenatal diagnosis in 167 cases, of which 59 cases were diagnosed by chorionic villi biopsy, 91 cases by amniotic fluid analysis, and 17 cases by cord blood analysis. Hb Bart's hydrops was detected by amplifying the break junction area of the alpha-thalassemia-1 Southeast Asia (SEA)-type gene, and beta-thalassemia major was detected by using naturally occurring restriction sites and the amplified created restriction sites (ACRS) method. Screening for hemoglobin (Hb) Bart's hydrops revealed 26 cases of Hb Bart's hydrops, 67 cases of alpha-thalassemia-1 (including 6 Hb Bart's hydrops falsely diagnosed as alpha-thalassemia-1 from chorionic villi samples), and 38 normal cases. Screening for beta-thalassemia major revealed 8 cases of beta-thalassemia major, 17 cases of beta-thalassemia minor, and 11 normal cases. In cases of alpha-thalassemia, maternal tissue contamination in the chorionic villi samples occurred in the diagnosis of the carrier state and further amniotic fluid analysis will be necessary. There were no any false-positive or false-negative results in beta-thalassemia major screening. We conclude that prenatal diagnosis is a reliable and accurate screening method for thalassemia and may be valuable in other areas of high prevalence for thalassemia in Southeast Asia and in Southern China.