Background. Wisconsin was severely affected by pandemic waves of 2009 influenza A H1N1 infection during the period 15 April through 30 August 2009 (wave 1) and 31 August 2009 through 2 January 2010 (wave 2).

Methods. To evaluate differences in epidemiologic features and outcomes during these pandemic waves, we examined prospective surveillance data on Wisconsin residents who were hospitalized ≥24 h with or died of pandemic H1N1 infection.

Results. Rates of hospitalizations and deaths from pandemic H1N1 infection in Wisconsin increased 4- and 5-fold, respectively, from wave 1 to wave 2; outside Milwaukee, hospitalization and death rates increased 10- and 8-fold, respectively. Hospitalization rates were highest among racial and ethnic minorities and children during wave 1 and increased most during wave 2 among non-Hispanic whites and adults. Times to hospital admission and antiviral treatment improved between waves, but the overall hospital course remained similar, with no change in hospitalization duration, intensive care unit admission, requirement for mechanical ventilation, or mortality.

Conclusions. We report broader geographic spread and marked demographic differences during pandemic wave 2, compared with wave 1, although clinical outcomes were similar. Our findings emphasize the importance of using comprehensive surveillance data to detect changing characteristics and impacts during an influenza pandemic and of vigorously promoting influenza vaccination and other prevention efforts.