BACKGROUND: The extent to which pandemic H1N1 influenza (pH1N1) differed from seasonal influenza remains uncertain. METHODS: By using active surveillance data collected by the Immunization Monitoring Program, Active at 12 Canadian pediatric hospitals, we compared characteristics of hospitalized children with pH1N1 with those with seasonal influenza A. We compared demographics, underlying health status, ICU admission, and mortality during both pandemic waves versus the 2004/2005 through the 2008/2009 seasons; influenza-related complications and hospitalization duration during pH1N1 wave 1 versus the 2004/2005 through the 2008/2009 seasons; and presenting signs and symptoms during both pH1N1 waves versus the 2006/2007 through the 2008/2009 seasons. RESULTS: We identified 1265 pH1N1 cases (351 in wave 1, 914 in wave 2) and 1319 seasonal influenza A cases (816 from 2006/2007 through 2008/2009). Median ages were 4.8 (pH1N1) and 1.7 years (seasonal influenza A); P < .0001. Preexisting asthma was overrepresented in pH1N1 relative to seasonal influenza A (13.8% vs 5.5%; adjusted P < .0001). Symptoms more often associated with pH1N1 wave 1 versus seasonal influenza A were cough, headache, and gastrointestinal symptoms (adjusted P < .01 for each symptom). pH1N1 wave 1 cases were more likely to have radiologically confirmed pneumonia (adjusted odds ratio = 2.1; 95% confidence interval = 1.1–3.8) and longer median length of hospital stay (4 vs 3 days; adjusted P = .003) than seasonal influenza A. Proportions of children requiring intensive care and deaths in both pH1N1 waves (14.6% and 0.6%, respectively) were not significantly different from the seasonal influenza A group (12.7% and 0.5%, respectively). CONCLUSIONS: pH1N1 in children differed from seasonal influenza A in risk factors, clinical presentation, and length of hospital stay, but not ICU admission or mortality.