Since new vaccines and anti-viral drugs for influenza have become available, collation of actual and country-specific epidemiological data is essential. Since respiratory syncytial virus (RSV) is a well known paediatric airway pathogen and some epidemiological data exist already, a comparison between influenza and RSV seems warranted. From July 1996 to June 2001 the naso-pharyngeal aspirates (NPA) of children from birth to 16 years of age, admitted to one of the two paediatric hospitals in Kiel, Germany, were investigated by a nine-valent multiplex reverse transcriptase PCR assay. NPA were investigated in 60·8% of 3469 children admitted with an acute respiratory tract infection. Community-acquired or nosocomial infections (in parentheses) due to influenza A were diagnosed in 122 (10) children, due to influenza B in 14 (2) and due to RSV in 325 (24) cases. Patients with influenza A (median 752 days) and influenza B (median 966 days) were older than patients with RSV (median 168 days). The spectrum of disease presentation was broader in influenza than in RSV. In each winter, admissions with influenza were less common than those with RSV. Influenza B only occurred in 2 of the 5 years. The cumulative, population-based incidences per 100 000 children 0–16 (0–5, >5–16) years of age were 53 (123, 22) for influenza A, 16 (30, 9) for influenza B and 165 (453, 4) for RSV. Cardiac conditions and asthma were the major risk factors for admission to hospital with influenza A (RR 9·8, 4·1) and RSV (8·5, 2·1) infections. Underlying conditions were most common in influenza B. Low gestational age doubled the risk for admission to hospital with influenza A infection, but did not show a dose–effect relationship as in RSV. The burden of influenza-positive hospitalizations was about one third that of RSV. The incidence was similar to reports from the United States. Targeting children with underlying conditions, especially cardiac conditions and asthma in the German immunization programme is appropriate, as long as no policy for vaccination of the general paediatric population exists.