Residents near concentrated animal feeding operations (CAFOs) have expressed concern about effects from associated air pollutants. Previous cross-sectional studies have found increased prevalence of asthma and wheezing among children who attend school near CAFOs. The Rural Air Pollutants and Children's Health (RAPCH) study used a school-based, longitudinal design to investigate acute respiratory responses in children attending public middle schools near CAFOs in eastern North Carolina. We conducted five sequential waves of data collection at three middle schools in February-November 2009. Each day in science class for 3-5 weeks, students completed a structured diary reporting current symptoms and recent odor observations, then measured their pulmonary function. We measured hydrogen sulfide (H<sub>2</sub>S) and particulate matter less than 10µm in diameter (PM<sub>10</sub>) at two locations: inside a participating classroom and outside the school building. The participatory protocol was designed to provide positive side effects for participants; process evaluation results from interviews with staff in May-June 2010 indicated benefits including increased interest in science, hands-on learning, and environmental awareness. 340 participants (95% participation) generated 5728 diary records (median=17). We used conditional linear fixed effects models to estimate within-person associations between air pollutant measures (12hr livestock odor, morning livestock odor, 12hr mean H<sub>2</sub>S, morning H<sub>2</sub>S, 12hr mean PM<sub>10</sub>, and morning PM<sub>10</sub>) and pulmonary function parameters (peak expiratory flow and forced expiratory volume in one second). There were substantial within-person decreases in pulmonary function over time-in-study. We found unexpected positive associations in unstratified analyses and larger beta coefficients with greater precision among students reporting wheeze at baseline. In analyses stratified by Week 1 versus Weeks 2-5 to control for time-in-study, we observed small beta coefficients with poor precision for all models. The RAPCH study had a positive impact on participants and their communities. We found minimal effects of airborne exposures from CAFOs on measured pulmonary function, however time-correlated measurement error, exposure definitions, or additional time-varying confounders may have obscured effects. Future analyses will examine symptom outcomes and explore the use of these data in cross-sectional designs to further characterize the potential impacts of air pollutants from CAFOs on children's respiratory health.