Great developments in the care of newborn infants have occured in the recent years and the survival rate of infants has increased significantly. However, there are many diseases which are still resistant to treatments and these infants end up with life-long morbidities. Treatment alternatives for these infants are very limited and stem cell transplantation is one of major advances in this regard. Stem cells are cells which have the capacity to regenerate themselves and differentiate to many cell types. These cells produce new cells for the cells which are ill, aged and dead and they act as if “spare parts” for the injured tissues. In recent years, these treatments have been used in newborns with chronic lung disease, hypoxic-ischemic encephalopathy and intracranial hemorrhages. However, these treatments can only be performed in highly specialized neonatal intensive care units with appropriate infrastructure and laboratory facilities as well as dedicated neonatology experts. In our University, stem cell transplantation was performed in a newborn infant with hypoxic-ischemic encephalopathy who was admitted to Prof. Suleyman Yalçın City Hospital Neonatal Intensive Care Unit. With this treatment the goal was tissue regeneration and prevention of inflammation which would lead to decreased brain injury. The neonatology team under the leadership of Prof. Fahri Ovalı, who is the Director of Department of Pediatrics and neonatologist performed the procedure under sterile conditions, after obtaining all the necessary approvals from the Ministry of Health and family. The infant is still under surveillance and is improving. This procedure was done for the first time in our University; however new treatments in new patients are expected.