A range of opportunistic pathogens cause infection after allogeneic stem cell transplantation. Adoptive immunotherapy has been shown to be effective for the prophylaxis and treatment of EBV and CMV infection, and the approach can theoretically be applied to other pathogens including adenovirus, varicella zoster virus, influenza A, HHV6 and BK virus as well as multiple fungi. In addition, it may be possible to utilise immune cells to target residual malignancy. Several questions remain including whether cell therapies should be used prophylactically, pre-emptively or as treatment for established infections and whether it is better to produce cell products from the original stem cell donor or use third party partially HLA matched normal donors as a source. Clinical trials suggest that if production and distribution methods can be simplified and streamlined, T cell therapies combined with other graft engineering strategies can improve outcomes in stem cell transplant patients.