The number of immunocompromised children in the population is increasing for a variety of reasons. Common respiratory viruses acquired in the community or in the hospital setting include the ortho- and paramyxoviruses and may cause severe lower respiratory tract disease in these children. Measles is again becoming a threat. Particularly in transplant patients, Herpes group viruses and adenoviruses, often part of a reactivation illness, can cause potentially life-threatening disease. The use of rapid molecular diagnostic techniques and an increasing array of antiviral therapies can help ensure a good outcome in many cases, although controlled clinical trial data are often lacking. Immunotherapeutic strategies using specific antibodies or cytotoxic T cells are being developed and are likely to have an increasing role in prophylaxis and pre-emptive therapy in the future. The development and introduction of vaccines against common respiratory diseases will help reduce the risks faced by these susceptible children.