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We sought to estimate the incidence of hospitalization attributable to influenza virus infection in Canadian children while controlling for the impact of other respiratory viruses.Hospital admissions for children and youth 0 to 19 years of age, 1994–2000, were modeled as a function of proxy variables for influenza, respiratory syncytial virus (RSV) and other respiratory viral activity, seasonality and trend, using a Poisson regression model with a linear link. These proxy variables were developed from influenza mortality and laboratory test results for influenza, RSV and other viruses. Various checks for consistency, model fit and robustness were conducted and guided model development.Overall, 1.5% of all pediatric respiratory admissions could be attributed to influenza (18 admissions per 100,000 per year). The largest burden was seen in infants 6 to 11 months of age with rates of 200 per 100,000 infants and approximately equivalent to the rate for adults aged 65 to 69. During peak influenza activity, 7% of respiratory admissions were attributable to influenza as were 35% of febrile seizure admissions. RSV and parainfluenza (PIV) were the major viral causes of hospital admission with rates of 130 and 160 per 100,000, respectively. Another 70 per 100,000 admissions were attributed to other influenza-like illnesses.Influenza is a significant cause of morbidity leading to hospitalization in Canadian children, particularly for those under 2 years of age. RSV, PIV and other respiratory viruses were found to be major causes of respiratory illness leading to hospital care, surpassing influenza.