Background: Deficient indoor environmental quality (IEQ) in schools could adversely affect the performance and physical health of students and teachers. Ventilation rate and particle filtration are two key factors that influence IEQ.Aims: We present the design and selected results of an intervention study conducted in two schools with 2nd to 4th grade students. We describe a number of innovative outcome measures for both academic performance and physical fitness.Methods: We conducted a blinded case-crossover trial of two interventions, increased ventilation rates and advanced particle filtration, in two primary schools. The school year was divided into five periods; a baseline period and four intervention periods, during which one-half of the classrooms was the treatment group; the other half was not. In each period, we measured IEQ parameters, e.g., optical particle counts (OPC), particulate matter (PM) concentrations, air change rates, volatile organic compounds (VOCs), in four classrooms in each school. Outcome measures, obtained on 629 students, included absenteeism, curriculum-based tests in several academic areas, and the progressive aerobic capacity endurance run (PACER) tests, which measures the cardio-respiratory endurance/aerobic capacity.Results: Interventions altered PM concentrations but did not appear substantially change estimated ventilation rates. We found that the PACER fitness scores varied little between treatment and control groups across intervention periods, but longitudinal analyses showed several changes. The interventions did not appear to alter absenteeism. Results for the two schools differed, possibly reflecting the ability to successfully implement interventions.Conclusions: The study suggests the potential of intervention studies in schools for identifying strategies that benefit indoor air quality and students' physical health, and suggests the need to control for time varying factors that may influence outcomes.