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The molecular basis and hematological phenotype of adult Thai β-thalassemia intermedia (β-TI) patients encountered with inferior vena cava (IVC) thrombosis were investigated. Hematological and molecular analysis revealed a trait previously not described. The disease was caused by interaction of the β(+)-thalassemia (β(+)-thal) gene with the -90 (C > T) (HBB: c.-140C > T) transition within the erythroid Krüppel-like factor (EKLF) binding site of the β-globin gene promoter with Hb E (HBB: c.79G > A) and α(+)-thalassemia (α(+)-thal). Hematological data of the patient were compared with those of heterozygous forms of these defects found in his family members and different genotype-phenotype interactions are illustrated. Globin gene haplotype analysis indicates an independent origin of this Thai β(+)-thal gene. Accurate diagnoses as well as knowledge of genotype-phenotype relationships were required for providing appropriate management of such cases.