Common complications in neonates occur in almost every organ system in the neonatal intensive care unit. While a number of them have short-term effects, a few of them also have long-term consequences. Among the latter are bronchopulmonary dysplasia and necrotizing enterocolitis in premature neonates, and hypoxic ischemic encephalopathy in borderline preterm and term neonates. While medical advances have improved our understanding of the pathogenesis, therapies to effectively prevent and/or significantly ameliorate the severity of these disorders, and to decrease their associated mortality and morbidity have not been found. One promising approach to make a potential impact in the outcomes of these neonatal conditions is the use stem cells, specifically, mesenchymal stem cells. The authors briefly review the potential role of stem cell therapy in the above-mentioned neonatal diseases. They focus primarily on human clinical trials.