The effects of antiretroviral (ARV) drugs administered to HIV-infected pregnancy on hematological parameters and hemoglobin (Hb) synthesis in ARV-exposed newborns with and without thalassemia carrier and of ARV drugs in worsening anemia in thalassemia carrier newborns are not well understood. Cord blood samples were collected from newborns of HIV-infected and -uninfected pregnancies. Hematological parameters and hemoglobin typing were analyzed by automated blood counter and capillary electrophoresis (CE), respectively. In the group of thalassemia carrier, the ARV-exposed newborns had significantly lower mean levels of red blood cell counts and hematocrit and had significantly higher mean levels of MCH than the ARV-unexposed newborns. Similar results were found in the group of newborns without thalassemia carrier. There were no statistical differences in mean levels of Hb-A₂, Hb-A, Hb-F and Hb-E (when applicable) in ARV-exposed and -unexposed newborns either with or without thalassemia carrier. However, ARV-exposed newborns who were thalassemia carriers had the lowest levels of hemoglobin and hematocrit when compared to the other groups. Therefore, ARV drugs used for prevention of HIV-mother-to-child transmission (HIV-MTCT) altered hematological parameters but did not affect hemoglobin synthesis in newborns with and without thalassemia carrier. However, thalassemia and ARV drugs might have synergetic effect in inducing severe anemia.