Hepatitis C virus and hepatitis B virus have a high transmission rate (blood or donor organ) and have a high incidence of progressive disease following organ grafting. Treatment of these viruses with interferon and other anti-viral agents is currently undergoing clinical trial. Cytomegalovirus infection or reactivation is well characterized and accurate reliable testing, treatment and prophylaxis are available. In lung and liver transplants cytomegalovirus shows a predilection for the transplanted organ and so has to be considered as part of the differential diagnosis of rejection. Epstein-Barr virus-induced post-transplant lymphoproliferative disorder is an important complication of transplantation requiring early diagnosis and prompt therapy if progression to a fatal disease is to be prevented.