Cellular immunity to viral and fungal antigens is often suppressed after stem cell transplantation. Viral infections, in particular infections with cytomegalovirus and Epstein-Barr virus, are often reactivated after allogeneic stem cell transplantation. Pathogenetic factors are immune deficiency and T-cell stimulation in the course of graft-versus-host reactions. Fungal infections are opportunistic infections derived with ubiquitous microorganisms. Immune deficiency, neutropenia, steroid treatment, and antibiotic treatment contribute to the pathogenesis. The study of viral and fungal immunity after allogeneic stem cell transplantation gives insight into the reconstitution of the immune system and tolerance.