Two preventative approaches exist to manage cytomegalovirus (CMV), a common infection in recipients of organ and stem cell transplants: prophylaxis--the prevention of viraemia--and pre-emptive therapy--the prevention of manifestation of disease in patients who have viraemia. Economic evaluation may provide a helpful framework to inform the choice between these two approaches. However, several issues arise. Direct comparisons of prophylaxis and pre-emptive therapy are rare and there are few epidemiological data that depict the full natural history of CMV infection and disease. There is a need for large, prospective randomised trials that directly compare these two strategies and are of sufficient duration to assess their overall impact on direct and indirect effects of CMV as well as patient quality of life. These methodological issues are relevant to the economic evaluation of preventative measures in other clinical settings and highlight the need for a rigorous evaluative framework to best inform decision making about the optimal strategy for patients.