Acute cytomegalovirus (CMV) disease and indirect effects caused by the virus alter the outcome after solid organ transplantation. Long-term results after 54 lung and 139 cardiac transplants at a single center have been retrospectively analyzed with regard to CMV status. Standard CMV prophylaxis consisted of ganciclovir for 100 days. Lung recipients were pretransplant CMV negative in 32 per cent as compared to heart recipients with 23 per cent. Patient survival after mismatch transplants (donor positive, recipient negative) was significantly reduced as compared to the other match groups (42% vs 76% at five years, P = 0.01). In heart recipients, CMV positive patients receiving a CMV negative graft showed best survival, whereas in the group of lung recipients negative/negative matched transplants produced best results. In both groups, CMV negative grafts had a better outcome than CMV positive grafts, and a survival difference between heart and lung recipients was only observed in recipients of a CMV positive grafts. Despite ganciclovir prophylaxis, CMV match remains an important factor for survival following heart and, even more profoundly, lung transplantation. Because survival was least favorable in the mismatched group, prophylactic regimens warrant improvement. For CMV negative lung recipients, CMV matching might be considered.