Hematopoietic stem-cell transplantation is associated with a profound immune deficiency manifested as an increased propensity to develop infections and probably also malignancies. Innate immunity, including epithelial barriers and phagocytes, typically recovers within weeks after grafting, and B-cell counts and CD8 T-cell counts recover within months. CD4 T-cell counts are low for years, and their recovery is particularly slow in older patients with poor thymic function. Therapies to improve immune function include vaccinations, immunoglobulins for recurrent infections, cytokines, and antigen-specific donor lymphocyte infusions.