Hematopoietic stem-cell transplantation (HSCT) has successfully been used to cure many pediatric disorders. However, the immunologic alterations associated with transplantation result in profound immunodeficiencies in the transplant recipient, resulting in significant infectious morbidity and mortality. The precarious process of immune reconstitution in the transplant recipient is neither instantaneous nor complete, but influenced by multiple factors such as graft-versus-host disease (GVHD), conditioning regimen, patient age and underlying disease. Studies in pediatric HSCT have revealed unique attributes of immune recovery in pediatric transplant recipients. Future studies addressing these findings are needed to complement novel immunotherapies emerging from the field of transplant immunology.