A seven-days-old male neonate was transferred to our institution in critically ill condition. Echocardiographic (ECHO) examination revealed the transposition of the great arteries (TGA) with a small ventricular septal defect. In the laboratory examination, arterial oxygen saturation was 29 percent and pH was 7.16, The poor condition of the neonate led us to decide to perform an immediate bedside balloon atrial septostomy (BAS) in the intensive care unit (ICU) with ECHO guidance. The umbilical vein was cannulated with a 5 Fr. Miller BAS catheter, Four balloon passes were performed resulting in large atrial septal defect. After the procedure, arterial oxygen saturation was measured at 40 percent. In TGA, the baby may present with severe hypoxia and may need management in the ICU. Emergency BAS may improve the clinical condition of the patient. Transferring the baby, who is mechanically ventilated (and is in openbed), to the catheterization laboratory takes time and can be harmful for him, and carries risk of extubation and heat loss.