Immunological recovery post-hematopoietic stem cell transplantation is variable. This depends upon the type of transplantation, source of hematopoietic stem cells for transplantation, prophylactic treatment for graft-versus-host disease and ongoing therapy for the treatment of graft-versus-host disease with immunosuppressive agents. Periodic numerical and functional assessment of recovery of the immune system after transplantation can identify the patients with inadequate immune system who are at risk for development of infectious complications. These patients should receive prophylactic therapy to decrease infection-related morbidity and mortality associated with transplantation procedures.