The reactivation of viruses from latency after allogeneic stem cell transplantation (SCT) continues to represent a major clinical challenge requiring sophisticated monitoring strategies in the context of prophylactic and/or preemptive antiviral drugs that are associated with significant expense, toxicity and rates of failure. Accumulating evidence has demonstrated the association of polyfunctional virus-specific T cells with protection from viral reactivation, affirmed by the ability of adoptively transferred virus-specific T cells to prevent and treat reactivation and disease. The roles of natural killer cells in early viral surveillance and of dendritic cells in priming of T cells have also been delineated. Most recently, a role for strain-specific humoral responses in preventing early cytomegalovirus (CMV) reactivation has been demonstrated in preclinical models. Despite these advances, many unknowns remain: what are the critical innate and adaptive responses over time; are the origin (eg, recipient vs donor) and localization (eg, in parenchymal tissue vs lymphoid organs) of these responses important; how does graft-versus-host disease and the prevention and treatment thereof (eg, high-dose steroids) affect the functionality and relevance of a particular immune axis; do the immune parameters that control latency, reactivation, and dissemination differ; and what is the impact of new antiviral drugs on the development of enduring antiviral immunity. Thus, although antiviral drugs have provided major improvements over the past two decades, understanding the immunological paradigms underpinning protective antiviral immunity after SCT offers the potential to generate nontoxic, immune-based therapeutic approaches for lasting protection from viral reactivation.