Thalassemia is a monogenic hematologic disease that has the highest prevalence globally. In addition, there is complexity of the genetic background associated with a variety of phenotypes presented among patients. Genetic heterogeneity related to fetal hemoglobin (HbF) production has been reported as an influencing phenotypic factor of β-thalassemia (β-thal). Therefore, this study aimed to find the effect of these genetic modifiers, especially in the XmnIlocus, rs11886868, rs766432 (BCL11A), and rs9399137 (HBS1L-MYB), among β-thal and HbE/β-thal patients in Indonesia, according to laboratory and clinical outcomes, including HbF levels and clinical scores. This study was also designed to compare these modifying effects among β-thal and HbE/β-thal patients in Indonesia.