Background: Information on the etiology and age-specific burden of respiratory viral infections among school-aged children remains limited. Methods: We conducted a cohort study to determine the etiology of ILI (influenza like illness) among 2,519 K-12 students during the 2012-13 influenza season. We obtained nasal swabs from students with ILI-related absences. Generalized linear mixed-effect regressions determined associations of outcomes, including ILI and laboratory-confirmed respiratory virus infection, with school grade and other covariates. Results: Overall, 459 swabs were obtained from 552 ILI-related absences. Respiratory viruses were found in 292 (63.6%) samples. Influenza was found in 189 (41.2%) samples. with influenza B found in 134 (70.9%). Rates of influenza B were significantly higher in grades 1 (10.1%, 95% CI 6.8%-14.4%), 2 (9.7%, 6.6%-13.6%), 3 (9.3%, 6.3%-13.2%), and 4 (9.9%, 6.8%-13.8%) than in kindergarteners (3.2%, 1.5%-6.0%). After accounting for grade, sex and self-reported vaccination status, influenza B infection risk was lower among kindergarteners in half-day programs compared to kindergarteners in full-day programs (OR = 0.19; 95% CI 0.08-0.45). Conclusions: ILI and influenza infection is concentrated in younger schoolchildren. Reduced infection by respiratory viruses is associated with a truncated school day for kindergarteners, but requires further investigation in other grades and populations.