We report a case of survival of homozygous α-thalassemia with aplasia/hypoplasia of phalanges and jejunal atresia. The occurrence of these malformations is consistent with the postulation that intra-uterine hypoxia due to the presence of hemoglobin Bart's (Hb Bart's) is the causative factor for the development of these malformations. There were two pitfalls in diagnosis: normal spun hematocrit level despite a low hemoglobin level and absence of hydropic features. Our case illustrated that nitric oxide and high frequency ventilation were ineffective in ameliorating persistent pulmonary hypertension of newborn until exchange transfusion was done replacing Hb Bart's with normal hemoglobin.