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Background: Canada experienced two distinct waves of pandemic (H1N1) influenza during the 2009 pandemic, one in the spring and the second in early fall 2009. We compared the incidence of hospital admissions and severe outcomes (admission to intensive care unit [ICU] and death) during the two waves. Methods: We reviewed data on all laboratory-confirmed cases of pandemic (H1N1) influenza that resulted in hospital admission, ICU admission or death reported to the Public Health Agency of Canada by all provinces and territories from Apr. 18, 2009, to Apr. 3, 2010. Results: A total of 8678 hospital admissions (including 1473 ICU admissions) and 428 deaths related to pandemic (H1N1) influenza were reported during the pandemic and post-peak period. There were 4.8 times more hospital admissions, 4.0 times more ICU admissions and 4.6 times more deaths in the second pandemic wave than in the first wave. ICU admissions and deaths as a proportion of hospital admissions declined in the second wave; there was a 16% proportional decline in ICU admissions and a 6% proportional decline in deaths compared with the first wave. Compared with patients admitted to hospital in the first wave, those admitted in the second wave were older (median age 30 v. 23 years) and more had underlying conditions (59.7% v. 47.5%). Pregnant women and Aboriginal people accounted for proportionally fewer patients who were admitted to hospital or who died in the second wave than in the first. Interpretation: The epidemiologic features of the first and second waves of the 2009 pandemic differed. The second wave was substantially larger and, although the patients admitted to hospital were older and more of them had underlying conditions, a smaller proportion had a severe outcome. [ABSTRACT FROM AUTHOR]