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Background: During the 2009 influenza pandemic in Korea, school-age children were mostly attacked by the novel influenza A virus (H1N1). Nevertheless, there is limited information on the cumulative incidence of the 2009 influenza pandemic among school populations. The aim of this study was to estimate the incidence of 2009 H1N1 influenza and influenza-like illness (ILI), and characterize the epidemiology among school-based populations in Korea Materials and Methods: This study analyzed the data collected by the daily school influenza reporting system for laboratory-confirmed influenza (H1N1 2009 pdm) and ILl in elementary, middle and high schools in Korea during the period, July 1 to December 20, 2009. Results: Between July 1 and December 20, 2009, a total of 525,668 cases of H1N1 2009 pdm were reported from the schools analyzed. The cumulative incidence of H1N1 2009 pdm was highest in elementary school children between 8 and 13 years of age (11,058 per 100,000 population), followed by middle school students between 14 and 16 years of age (10,080 per 100,000), and high school students between 17 and 19 years of age (8,886 per 100,000). With the alignment of the epidemic curves by the three levels of school education, the age group-specific differences in the timing of the infection became apparent. The infections peaked 1 week earlier in both middle and high school students (November 3, 2009) than in elementary school children (November 10, 2009). The infections occurred an average of 7.3 [95% confidence interval(CI): 7.2-7.4] and 3.4 (95% CI: 3.3-3.5) days earlier in the middle and high school students, respectively, than elementary school children (P<0.001). The overall trend of the epidemic waves from the school reporting system data was similar to that of the national surveillance date from the Korea Centers for Disease Control and Prevention. Conclusions: This study suggests that during the 2009 pandemic, one student in every 10 was infected with H1N1 2009 pdm, which is double that estimated from the national surveillance data. In addition, middle and high school students were important drivers of H1N1 2009 pdm transmission in 2009. During the 2009 influenza pandemic, the daily school reporting system provided valuable information for estimating the incidence as well as the epidemiological characteristics in school-based populations. [ABSTRACT FROM AUTHOR]