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We describe hematologic and molecular characteristics of a hitherto undescribed interaction between the Filipino deletional β0-thalassemia with Hb E and α-thalassemia in a Thai family. This study was conducted during the prenatal screening of a pregnant Thai woman and her family members. A prenatal diagnosis was performed at her second pregnancy by amniocentesis. Laboratory investigations identified that the pregnant woman was Hb E heterozygote with α+-thalassemia, whereas her husband was a double heterozygote for the Filipino deletional β0-thalassemia and α+-thalassemia. Their affected son was a patient with a previously undescribed condition of Hb E-β0-thalassemia with α+-thalassemia. Both a combined gap-polymerase chain reaction (PCR) and allele-specific PCR were used successfully in the prenatal diagnosis, which identified an affected fetus with Hb E-β0-thalassemia without α+-thalassemia. Beta globin gene haplotype analysis indicated the same origin of this Filipino β0-thalassemia in Asian populations.