Epstein-Barr (EBV) and Adenovirus (AdV) viral infections represent a significant cause of morbi-mortality in allogeneic hematopoietic stem cell transplantation recipients due to the use of immunomyelosuppressive treatments and the prolonged period of immunodeficiency that they generate. To date, the post-transplant protective role of EBV and AdV specific CD8+ T lymphocytes (CTLs) has been demonstrated. However, other factors are increasingly important in regulating the reconstitution and activity of CTLs specific to these viruses such as different cell subpopulations (CD4 + T lymphocytes, regulatory T lymphocytes, dendritic cells, Natural Killer cells, etc.), molecular mechanisms of immunoregulation and the drugs administered to the patient as prophylaxis for a possible graft-versus-host disease. The aim of this review is to analyze the importance of monitoring the functional EBV and AdV-specific cellular response in the management of post-transplant recipients.